CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields (scientific article)

cites work (P2860)

Q47567836	"Divide and conquer" semiclassical molecular dynamics: A practical method for spectroscopic calculations of high dimensional molecular systems
Q47563921	"Star" morphologies of charged nanodrops comprised of conformational isomers
Q36917090	1,3-Propanediol binds inside the water-conducting pore of aquaporin 4: Does this efficacious inhibitor have sufficient potency?
Q39722915	1,3-propanediol binds deep inside the channel to inhibit water permeation through aquaporins
Q48208968	1.14*CM1A-LBCC: Localized Bond-Charge Corrected CM1A Charges for Condensed-Phase Simulations
Q50891803	2D lattice model of a lipid bilayer: Microscopic derivation and thermodynamic exploration.
Q85928946	A Combined Molecular Docking/Dynamics Approach to Probe the Binding Mode of Cancer Drugs with Cytochrome P450 3A4
Q37701700	A Comparative Study of Transferable Aspherical Pseudoatom Databank and Classical Force Fields for Predicting Electrostatic Interactions in Molecular Dimers
Q57810877	A Comparison of QM/MM Simulations with and without the Drude Oscillator Model Based on Hydration Free Energies of Simple Solutes
Q64114044	A Complete Assessment of Dopamine Receptor- Ligand Interactions through Computational Methods
Q89856883	A Computational Pipeline to Predict Cardiotoxicity:From the Atom to the Rhythm
Q92495421	A Machine Learning Approach for the Discovery of Ligand-Specific Functional Mechanisms of GPCRs
Q64080503	A Molecular Dynamics Approach to Explore the Intramolecular Signal Transduction of PPAR-α
Q99591097	A Novel Cytotoxic Conjugate Derived from the Natural Product Podophyllotoxin as a Direct-Target Protein Dual Inhibitor
Q58109303	A Novel Integrated Way for Deciphering the Glycan Code for the FimH Lectin
Q89967404	A Pilot Study of All-Computational Drug Design Protocol-From Structure Prediction to Interaction Analysis
Q48125440	A Rationally Designed, General Strategy for Membrane Orientation of Photoinduced Electron Transfer-Based Voltage-Sensitive Dyes.
Q41869613	A comparative Kirkwood-Buff study of aqueous methanol solutions modeled by the CHARMM additive and Drude polarizable force fields.
Q36416521	A computational assessment of the permeability and salt rejection of carbon nanotube membranes and their application to water desalination
Q36429363	A designed inhibitor of a CLC antiporter blocks function through a unique binding mode
Q99559831	A dynamic simulation study of FDA drug from zinc database against COVID-19 main protease receptor
Q58795948	A fast and accurate computational method for the linear-combination-based isotropic periodic sum
Q33782655	A fixed-charge model for alcohol polarization in the condensed phase, and its role in small molecule hydration
Q37240626	A gating mechanism of pentameric ligand-gated ion channels
Q55259094	A halogen bond-mediated highly active artificial chloride channel with high anticancer activity.
Q34467065	A highly tilted membrane configuration for the prefusion state of synaptobrevin
Q90468092	A mechanism for the activation of the mechanosensitive Piezo1 channel by the small molecule Yoda1
Q33781359	A membrane-embedded pathway delivers general anesthetics to two interacting binding sites in the Gloeobacter violaceus ion channel
Q37238636	A model of peptide triazole entry inhibitor binding to HIV-1 gp120 and the mechanism of bridging sheet disruption
Q92582746	A model to study the inhibition of nsP2B-nsP3 protease of dengue virus with imidazole, oxazole, triazole thiadiazole, and thiazolidine based scaffolds
Q42416282	A molecular propeller effect for chiral separation and analysis
Q99608008	A mutant form of ERα associated with estrogen insensitivity affects the coupling between ligand binding and coactivator recruitment
Q58581343	A mutational and molecular dynamics study of the cys-loop GABA receptor Hco-UNC-49 from Haemonchus contortus: Agonist recognition in the nematode GABA receptor family
Q48045574	A neural-network potential through charge equilibration for WS2: From clusters to sheets.
Q97423533	A novel diterpene agent isolated from Microbispora hainanensis strain CSR-4 and its in vitro and in silico inhibition effects on acetylcholine esterase enzyme
Q33867220	A novel method for constructing continuous intrinsic surfaces of nanoparticles
Q93103311	A structural model of the human serotonin transporter in an outward-occluded state
Q40132165	A two-helix motif positions the lysophosphatidic acid acyltransferase active site for catalysis within the membrane bilayer
Q28465578	ACPYPE - AnteChamber PYthon Parser interfacE
Q35040558	AUTOMATED FORCE FIELD PARAMETERIZATION FOR NON-POLARIZABLE AND POLARIZABLE ATOMIC MODELS BASED ON AB INITIO TARGET DATA
Q51569821	Ab initio parameterization of YFF1, a universal force field for drug-design applications.
Q47567527	Absolute binding free energies for octa-acids and guests in SAMPL5 : Evaluating binding free energies for octa-acid and guest complexes in the SAMPL5 blind challenge.
Q57463690	Absolute binding free energies for the SAMPL6 cucurbit[8]uril host-guest challenge via the AMOEBA polarizable force field
Q47567557	Absolute binding free energy calculations of CBClip host-guest systems in the SAMPL5 blind challenge.
Q28385662	Absolute free energy of binding of avidin/biotin, revisited
Q57289886	Accelerating QM/MM Free Energy Computations via Intramolecular Force Matching
Q35926185	Accelerating membrane insertion of peripheral proteins with a novel membrane mimetic model.
Q47263447	Accelerating potential of mean force calculations for lipid membrane permeation: System size, reaction coordinate, solute-solute distance, and cutoffs
Q92489506	Accuracy evaluation and addition of improved dihedral parameters for the MMFF94s
Q52655826	Accurate PDZ/Peptide Binding Specificity with Additive and Polarizable Free Energy Simulations.
Q90663132	Acetyl-CoA-mediated activation of Mycobacterium tuberculosis isocitrate lyase 2
Q36990877	Activation and dynamic network of the M2 muscarinic receptor
Q46858789	Activation mechanisms of the first sphingosine-1-phosphate receptor
Q93106406	Activation of PKA via asymmetric allosteric coupling of structurally conserved cyclic nucleotide binding domains
Q46246183	Active-site plasticity revealed in the asymmetric dimer of AnPrx6 the 1-Cys peroxiredoxin and molecular chaperone from Anabaena sp. PCC 7210.
Q41438539	Acyl-2-aminobenzimidazoles: a novel class of neuroprotective agents targeting mGluR5
Q39290921	Additive CHARMM force field for naturally occurring modified ribonucleotides
Q42097264	Aggregation behavior of ibuprofen, cholic acid and dodecylphosphocholine micelles
Q35926130	Agonist dynamics and conformational selection during microsecond simulations of the A(2A) adenosine receptor
Q46205951	Albumin/vaccine nanocomplexes that assemble in vivo for combination cancer immunotherapy.
Q37481801	All the O2 Consumed by Thermus thermophilus Cytochrome ba3 Is Delivered to the Active Site through a Long, Open Hydrophobic Tunnel with Entrances within the Lipid Bilayer
Q28833669	All-Atom Molecular Dynamics of Virus Capsids as Drug Targets
Q43021666	All-atom structures and calcium binding sites of the bacterial photosynthetic LH1-RC core complex from Thermochromatium tepidum.
Q47276709	Allosteric Control of a Plant Receptor Kinase through S-Glutathionylation
Q57044300	Allosteric Effects of the Proton Donor on the Microbial Proton Pump Proteorhodopsin
Q91746784	Allosteric Interactions in Human Cytochrome P450 CYP3A4: The Role of Phenylalanine 213
Q57050158	Allosteric Role of Substrate Occupancy Toward the Alignment of P-glycoprotein Nucleotide Binding Domains
Q37270339	Allosteric activation of SENP1 by SUMO1 β-grasp domain involves a dock-and-coalesce mechanism.
Q64258152	Allosteric enhancement of ORP1-mediated cholesterol transport by PI(4,5)P/PI(3,4)P
Q35333600	Allosteric inhibitors have distinct effects, but also common modes of action, in the HCV polymerase
Q38736870	Allosteric modulation model of the mu opioid receptor by herkinorin, a potent not alkaloidal agonist
Q47565964	Allosteric modulation of human dopamine transporter activity under conditions promoting its dimerization.
Q63990932	Allysine modifications perturb tropoelastin structure and mobility on a local and global scale
Q28834286	An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications
Q47554737	An Improved Method for Magnetic Nanocarrier Drug Delivery across the Cell Membrane
Q91964281	An Integrated Pan-Cancer Analysis and Structure-Based Virtual Screening of GPR15
Q42382077	An efficient protocol for obtaining accurate hydration free energies using quantum chemistry and reweighting from molecular dynamics simulations
Q60961473	An efficient strategy to estimate thermodynamics and kinetics of G protein-coupled receptor activation using metadynamics and maximum caliber
Q64110933	An experimentally validated approach to calculate the blood-brain barrier permeability of small molecules
Q55032329	Analogs of the Scorpion Venom Peptide Stigmurin: Structural Assessment, Toxicity, and Increased Antimicrobial Activity.
Q40973806	Analysis of positive and negative allosteric modulation in metabotropic glutamate receptors 4 and 5 with a dual ligand.
Q33687719	Angiotensin II type 1/adenosine A 2A receptor oligomers: a novel target for tardive dyskinesia
Q64980510	Anti-Correlation between the Dynamics of the Active Site Loop and C-Terminal Tail in Relation to the Homodimer Asymmetry of the Mouse Erythroid 5-Aminolevulinate Synthase.
Q64082927	Anti-HIV-1 integrase potency of methylgallate from Alchornea cordifolia using in vitro and in silico approaches
Q28538336	Anti-prion activity of a panel of aromatic chemical compounds: in vitro and in silico approaches
Q58641877	Antibacterial Activity of Teixobactin Derivatives on Clinically Relevant Bacterial Isolates
Q36074450	Application of a BOSS-Gaussian interface for QM/MM simulations of Henry and methyl transfer reactions
Q39597289	Application of binding free energy calculations to prediction of binding modes and affinities of MDM2 and MDMX inhibitors
Q95841339	Application of the Brown dynamics fluctuation-dissipation theorem to the study of Plasmodium berghei transporter protein PbAQP
Q47205069	Aqueous ionic liquids influence the disulfide bond isoform equilibrium in conotoxin AuIB: a consequence of the Hofmeister effect?
Q46249034	Arachidonic Acid Metabolism by Human Cardiovascular CYP2J2 Is Modulated by Doxorubicin.
Q98728943	Arginine methylation of SHANK2 by PRMT7 promotes human breast cancer metastasis through activating endosomal FAK signalling
Q98293359	Artificial Intracellular Filaments
Q36385181	Aspheric Solute Ions Modulate Gold Nanoparticle Interactions in an Aqueous Solution: An Optimal Way To Reversibly Concentrate Functionalized Nanoparticles
Q91034551	Assessing the Predictive Power of Relative Binding Free Energy Calculations for Test Cases Involving Displacement of Binding Site Water Molecules
Q89928274	Assessing the accuracy of octanol-water partition coefficient predictions in the SAMPL6 Part II log P Challenge
Q30427012	Assessing the accuracy of the general AMBER force field for 2,2,2-trifluoroethanol as solvent
Q34537730	Assessing the quality of absolute hydration free energies among CHARMM-compatible ligand parameterization schemes
Q33847044	Assessment of the transferability of a protein force field for the simulation of peptide-surface interactions
Q34543355	Association of alkanes with the aqueous liquid-vapor interface: a reference system for interpreting hydrophobicity generally through interfacial fluctuations.
Q41429574	Asymmetric Binding and Metabolism of Polyunsaturated Fatty Acids (PUFAs) by CYP2J2 Epoxygenase.
Q36638888	Asymmetric ligand binding facilitates conformational transitions in pentameric ligand-gated ion channels
Q42375557	Atomic mutagenesis in ion channels with engineered stoichiometry
Q59808200	Atomistic Model for Simulations of the Sedative Hypnotic Drug 2,2,2-Trichloroethanol
Q34394221	Atomistic models of general anesthetics for use in in silico biological studies
Q36804366	Augmenting drug-carrier compatibility improves tumour nanotherapy efficacy
Q42199119	Automation of the CHARMM General Force Field (CGenFF) I: bond perception and atom typing.
Q42184293	Automation of the CHARMM General Force Field (CGenFF) II: assignment of bonded parameters and partial atomic charges.
Q34445710	Back to the future: can physical models of passive membrane permeability help reduce drug candidate attrition and move us beyond QSPR?
Q42020428	Balancing target flexibility and target denaturation in computational fragment-based inhibitor discovery
Q42086540	Base flip in DNA studied by molecular dynamics simulationsof differently-oxidized forms of methyl-Cytosine
Q90929703	Bases of Bacterial Sodium Channel Selectivity Among Organic Cations
Q35928904	Beyond modeling: all-atom olfactory receptor model simulations
Q91156903	Biased Agonist TRV027 Determinants in AT1R by Molecular Dynamics Simulations
Q43063613	Biasing Potential Replica Exchange Multisite λ-Dynamics for Efficient Free Energy Calculations
Q42179736	Bilayer-Mediated Structural Transitions Control Mechanosensitivity of the TREK-2 K2P Channel.
Q36344868	Binding enthalpy calculations for a neutral host-guest pair yield widely divergent salt effects across water models.
Q35450396	Binding hotspots on K-ras: consensus ligand binding sites and other reactive regions from probe-based molecular dynamics analysis
Q38743944	Binding mode analyses of NAP derivatives as mu opioid receptor selective ligands through docking studies and molecular dynamics simulation
Q55092101	Binding, Thermodynamics, and Selectivity of a Non-peptide Antagonist to the Melanocortin-4 Receptor.
Q41682691	Biochemical and biophysical characterization of Leishmania donovani gamma-glutamylcysteine synthetase
Q35779780	Biomimetics: From Bioinformatics to Rational Design of Dendrimers as Gene Carriers.
Q28109324	Biomolecular interactions modulate macromolecular structure and dynamics in atomistic model of a bacterial cytoplasm
Q48054550	Blind prediction of distribution in the SAMPL5 challenge with QM based protomer and pK a corrections
Q34257034	Blind prediction of host-guest binding affinities: a new SAMPL3 challenge.
Q36276935	Boramino acid as a marker for amino acid transporters
Q89612677	Boron nitride nanotubes as containers for targeted drug delivery of doxorubicin
Q28545199	Breaking the hydrophobicity of the MscL pore: insights into a charge-induced gating mechanism
Q27902346	Bringing the MMFF force field to the RDKit: implementation and validation
Q36602196	C60 fullerene localization and membrane interactions in RAW 264.7 immortalized mouse macrophages.
Q47694932	CDOCKER and λ-dynamics for prospective prediction in D₃R Grand Challenge 2.
Q42105857	CHARMM Additive All-Atom Force Field for Phosphate and Sulfate Linked to Carbohydrates
Q28817182	CHARMM Force Field Parameterization of Peroxisome Proliferator-Activated Receptor γ Ligands
Q34085563	CHARMM additive all-atom force field for carbohydrate derivatives and its utility in polysaccharide and carbohydrate-protein modeling.
Q33693774	CHARMM additive all-atom force field for glycosidic linkages in carbohydrates involving furanoses.
Q30365988	CHARMM additive and polarizable force fields for biophysics and computer-aided drug design
Q38793733	CHARMM-GUI 10 years for biomolecular modeling and simulation
Q36461179	CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field
Q36569443	CHARMM-GUI Ligand Binder for absolute binding free energy calculations and its application
Q36539936	CHARMM-GUI PDB manipulator for advanced modeling and simulations of proteins containing nonstandard residues.
Q48061728	CHARMM-GUI ligand reader and modeler for CHARMM force field generation of small molecules
Q36010254	CSM-lig: a web server for assessing and comparing protein-small molecule affinities.
Q36864487	Calcium causes a conformational change in lamin A tail domain that promotes farnesyl-mediated membrane association
Q93234511	Calcium-Induced Lipid Nanocluster Structures: Sculpturing of the Plasma Membrane
Q45710657	Calculating binding free energies of host-guest systems using the AMOEBA polarizable force field
Q57397675	Calculating distribution coefficients based on multi-scale free energy simulations: an evaluation of MM and QM/MM explicit solvent simulations of water-cyclohexane transfer in the SAMPL5 challenge
Q28396455	Calculation of the Absolute Free Energy of Binding and Related Entropies with the HSMD-TI Method: The FKBP12-L8 Complex
Q42695127	Calculation of the Vibrational Stark Effect Using a First-Principles QM/MM Approach
Q36169609	Campomanesia adamantium Peel Extract in Antidiarrheal Activity: The Ability of Inhibition of Heat-Stable Enterotoxin by Polyphenols
Q45934140	Can Relative Binding Free Energy Predict Selectivity of Reversible Covalent Inhibitors?
Q33358174	Can molecular dynamics and QM/MM solve the penicillin binding protein protonation puzzle?
Q64258219	Cannabinoid Receptor 2 Agonist JWH-015 Inhibits Interleukin-1β-Induced Inflammation in Rheumatoid Arthritis Synovial Fibroblasts and in Adjuvant Induced Arthritis Rat via Glucocorticoid Receptor
Q36021827	Cannabinoids suppress inflammatory and neuropathic pain by targeting α3 glycine receptors.
Q37292440	Capturing Spontaneous Membrane Insertion of the Influenza Virus Hemagglutinin Fusion Peptide
Q35008535	Capturing spontaneous partitioning of peripheral proteins using a biphasic membrane-mimetic model
Q54942086	Catalytic mechanism and molecular engineering of quinolone biosynthesis in dioxygenase AsqJ.
Q90612725	Cation-π Interactions between Methylated Ammonium Groups and Tryptophan in the CHARMM36 Additive Force Field
Q35206344	Challenges, applications, and recent advances of protein-ligand docking in structure-based drug design.
Q90640227	Characterisation of aptamer-anchored poly(EDMA-co-GMA) monolith for high throughput affinity binding
Q48157940	Characterization of Conformational Ensembles of Protonated N-glycans in the Gas-Phase
Q42394672	Characterization of the Local Structure in Liquid Water by Various Order Parameters
Q36928692	Characterizing the membrane-bound state of cytochrome P450 3A4: structure, depth of insertion, and orientation
Q52659146	Chemical Space Expansion of Bromodomain Ligands Guided by in Silico Virtual Couplings (AutoCouple).
Q47858853	Chemical substitutions in the selectivity filter of potassium channels do not rule out constricted-like conformations for C-type inactivation.
Q57155445	Chiral Separation via Molecular Sieving: A Computational Screening of Suitable Functionalizations for Nanoporous Graphene
Q92516951	Chlorogenic acid isomers directly interact with Keap 1-Nrf2 signaling in Caco-2 cells
Q43070060	Chloroperoxidase-catalyzed epoxidation of cis-β-methylstyrene: distal pocket flexibility tunes catalytic reactivity
Q44773893	Classification of the ejection mechanisms of charged macromolecules from liquid droplets
Q96162980	Clearance of activity-evoked K+ transients and associated glia cell swelling occur independently of AQP4: A study with an isoform-selective AQP4 inhibitor
Q43025545	Cloning, expression, and molecular dynamics simulations of a xylosidase obtained from Thermomyces lanuginosus
Q92974812	Cluster Formation of Polyphilic Molecules Solvated in a DPPC Bilayer
Q96303545	Co-crystal Structure of Thermosynechococcus elongatus Sucrose Phosphate Synthase With UDP and Sucrose-6-Phosphate Provides Insight Into Its Mechanism of Action Involving an Oxocarbenium Ion and the Glycosidic Bond
Q41962593	Coarse-grained simulations of the HIV-1 matrix protein anchoring: revisiting its assembly on membrane domains
Q89893266	Coexistence of Lipid Phases Stabilizes Interstitial Water in the Outer Layer of Mammalian Skin
Q47923085	Coexisting origins of subdiffusion in internal dynamics of proteins
Q108768061	Combining Machine Learning and Computational Chemistry for Predictive Insights Into Chemical Systems
Q88601613	Combining the polarizable Drude force field with a continuum electrostatic Poisson-Boltzmann implicit solvation model
Q37630653	Comparative Study of the Collective Dynamics of Proteins and Inorganic Nanoparticles
Q30386769	Comparing pharmacophore models derived from crystal structures and from molecular dynamics simulations
Q90589217	Comparison of Carbohydrate Force Fields Using Gaussian Accelerated Molecular Dynamics Simulations and Development of Force Field Parameters for Heparin-Analogue Pentasaccharides
Q92935782	Comparison of Charge Derivation Methods Applied to Amino Acid Parameterization
Q36706730	Comparison of Three Chain-of-States Methods: Nudged Elastic Band and Replica Path with Restraints or Constraints
Q47970683	Comparison of simulation and experimental results for a model aqueous tert-butanol solution
Q57463686	Comparison of the umbrella sampling and the double decoupling method in binding free energy predictions for SAMPL6 octa-acid host-guest challenges
Q30372639	Complete atomistic model of a bacterial cytoplasm for integrating physics, biochemistry, and systems biology.
Q90407504	Comprehensive Assessment of Torsional Strain in Crystal Structures of Small Molecules and Protein-Ligand Complexes using ab Initio Calculations
Q37607031	Computation of Hydration Free Energies Using the Multiple Environment Single System Quantum Mechanical/Molecular Mechanical Method
Q64113077	Computational Estimation of Microsecond to Second Atomistic Folding Times
Q57492142	Computational Insight Into Vitamin K ω-Hydroxylation by Cytochrome P450 4F2
Q36741836	Computational Investigation of the Effect of Lipid Membranes on Ion Permeation in Gramicidin A.
Q40243231	Computational Models for Predictive Cardiac Ion Channel Pharmacology.
Q36552694	Computational Studies of Molecular Permeation through Connexin26 Channels
Q26746941	Computational approaches in target identification and drug discovery
Q92980877	Computational evolution of an RNA-binding protein towards enhanced oxidized-RNA binding
Q47348549	Computational insights into the G-protein-biased activation and inactivation mechanisms of the μ opioid receptor
Q44349926	Computational insights into the subtype selectivity and "message-address-efficacy" mechanisms of opioid receptors through JDTic binding and unbinding
Q35069159	Computational ligand-based rational design: Role of conformational sampling and force fields in model development.
Q61799587	Computational screening of medicinal plant phytochemicals to discover potent pan-serotype inhibitors against dengue virus
Q91525393	Computational screening of nanoparticles coupling to Aβ40 peptides and fibrils
Q50278028	Computational solvation dynamics of oxyquinolinium betaine linked to trehalose.
Q27350315	Computational studies of the binding profile of phosphoinositide PtdIns (3,4,5) P₃ with the pleckstrin homology domain of an oomycete cellulose synthase
Q85679997	Computational study enlightens the structural role of the alcohol acyltransferase DFGWG motif
Q50112390	Computational study of the DPAP molecular rotor in various environments: from force field development to molecular dynamics simulations and spectroscopic calculations.
Q47373679	Computer simulations of alkali-acetate solutions: Accuracy of the forcefields in difference concentrations.
Q90131372	Computer simulations of protein-membrane systems
Q51311450	Computer-Aided Drug Design Methods.
Q47130531	Computer-Aided Drug Discovery in Plant Pathology
Q39671868	Computer-aided drug design guided by hydrogen/deuterium exchange mass spectrometry: A powerful combination for the development of potent and selective inhibitors of Group VIA calcium-independent phospholipase A2.
Q40543300	Computing Protein-Protein Association Affinity with Hybrid Steered Molecular Dynamics
Q92613345	Computing Relative Binding Affinity of Ligands to Receptor: An Effective Hybrid Single-Dual-Topology Free-Energy Perturbation Approach in NAMD
Q42412958	Computing membrane-AQP5-phosphatidylserine binding affinities with hybrid steered molecular dynamics approach
Q48507949	Computing osmotic permeabilities of aquaporins AQP4, AQP5, and GlpF from near-equilibrium simulations.
Q51227911	Computing the binding affinity of a ligand buried deep inside a protein with the hybrid steered molecular dynamics.
Q35027093	Concurrent cooperativity and substrate inhibition in the epoxidation of carbamazepine by cytochrome P450 3A4 active site mutants inspired by molecular dynamics simulations
Q37095634	Conformational Heterogeneity in the Michaelis Complex of Lactate Dehydrogenase: An Analysis of Vibrational Spectroscopy Using Markov and Hidden Markov Models
Q44341109	Conformational Heterogeneity of Intracellular Loop 3 of the μ-opioid G-protein Coupled Receptor
Q34424004	Conformational dynamics in human purine nucleoside phosphorylase with reactants and transition-state analogues
Q48333250	Conformational dynamics of cathepsin D and binding to a small-molecule BACE1 inhibitor.
Q38944603	Conformational energy range of ligands in protein crystal structures: The difficult quest for accurate understanding
Q37206494	Conformational freedom in tight binding enzymatic transition-state analogues
Q89517720	Conformational spread and dynamics in allostery of NMDA receptors
Q37596310	Conopeptide Vt3.1 preferentially inhibits BK potassium channels containing β4 subunits via electrostatic interactions.
Q41835961	Consensus 3D model of μ-opioid receptor ligand efficacy based on a quantitative Conformationally Sampled Pharmacophore.
Q40295980	Conserved residues of the Pro103-Arg115 loop are involved in triggering the allosteric response of the Escherichia coli ADP-glucose pyrophosphorylase.
Q47136224	Constant pH Molecular Dynamics Reveals pH-Modulated Binding of Two Small-Molecule BACE1 Inhibitors.
Q33803513	Control of protein orientation on gold nanoparticles
Q41662444	Controlling Protein Surface Orientation by Strategic Placement of Oligo-Histidine Tags
Q48122237	Conversion between parallel and antiparallel β-sheets in wild-type and Iowa mutant Aβ40 fibrils.
Q35118400	Correcting for the free energy costs of bond or angle constraints in molecular dynamics simulations
Q92542509	Could Quantum Mechanical Properties Be Reflected on Classical Molecular Dynamics? The Case of Halogenated Organic Compounds of Biological Interest
Q54935867	Counting charges on membrane-bound peptides.
Q45063604	Coupled-cluster based approach for core-level states in condensed phase: Theory and application to different protonated forms of aqueous glycine.
Q47623218	Coupling X-Ray Reflectivity and In Silico Binding to Yield Dynamics of Membrane Recognition by Tim1.
Q92133857	Cryptic pocket formation underlies allosteric modulator selectivity at muscarinic GPCRs
Q27681780	Crystal Structure of Cindoxin, the P450cin Redox Partner
Q46266293	Crystal Structure of an LSD-Bound Human Serotonin Receptor
Q27677132	Crystal structure of a eukaryotic phosphate transporter
Q36010677	Current status of protein force fields for molecular dynamics simulations
Q34568152	Cy3-DNA stacking interactions strongly depend on the identity of the terminal basepair
Q51739416	Cytochrome aa3 Oxygen Reductase Utilizes the Tunnel Observed in the Crystal Structures To Deliver O2 for Catalysis.
Q27317439	Cytoplasmic dynein binding, run length, and velocity are guided by long-range electrostatic interactions
Q42126126	Cytosine methylation at CpCpG sites triggers accumulation of non-CpG methylation in gene bodies.
Q46445025	D4 dopamine receptor high-resolution structures enable the discovery of selective agonists.
Q38527937	DIRECT-ID: An automated method to identify and quantify conformational variations--application to β2 -adrenergic GPCR.
Q36817989	De novo reconstruction of DNA origami structures through atomistic molecular dynamics simulation
Q92730507	Deciphering the Molecular Recognition Mechanism of Multidrug Resistance Staphylococcus aureus NorA Efflux Pump Using a Supervised Molecular Dynamics Approach
Q34236107	Decoding the signaling of a GPCR heteromeric complex reveals a unifying mechanism of action of antipsychotic drugs.
Q36107403	Deconstructing 14-phenylpropyloxymetopon: minimal requirements for binding to mu opioid receptors
Q47993096	DelPhiForce, a tool for electrostatic force calculations: Applications to macromolecular binding
Q96123075	Delicate Balance of Non-Covalent Forces Govern the Biocompatibility of Graphitic Carbon Nitride towards Genetic Materials
Q88758182	Dendritic PEG outer shells enhance serum stability of polymeric micelles
Q34296290	Derivation of coarse-grained potentials via multistate iterative Boltzmann inversion.
Q38295078	Design and evaluation of an apta-nano-sensor to detect Acetamiprid in vitro and in silico.
Q33564915	Detection of lipid-induced structural changes of the Marburg virus matrix protein VP40 using hydrogen/deuterium exchange-mass spectrometry
Q60469347	Determination of key receptor–ligand interactions of dopaminergic arylpiperazines and the dopamine D2 receptor homology model
Q36915324	Determination of partial molar volumes from free energy perturbation theory
Q64114317	Determining selection free energetics from nucleotide pre-insertion to insertion in viral T7 RNA polymerase transcription fidelity control
Q90139077	Development and Validation of the Quantum Mechanical Bespoke Protein Force Field
Q47716175	Development of CHARMM-Compatible Force-Field Parameters for Cobalamin and Related Cofactors from Quantum Mechanical Calculations.
Q41538383	Development of Fluorescent Probes that Target Serotonin 5-HT2B Receptors
Q30785490	Development of Potent and Selective Inhibitors for Group VIA Calcium-Independent Phospholipase A2 Guided by Molecular Dynamics and Structure-Activity Relationships
Q35096802	Development of the CHARMM Force Field for Lipids
Q49957155	Digging into Lipid Membrane Permeation for Cardiac Ion Channel Blocker d-Sotalol with All-Atom Simulations.
Q90730841	Dipolar induced spin-lattice relaxation in the myelin sheath: A molecular dynamics study
Q34998116	Direct evidence for methyl group coordination by carbon-oxygen hydrogen bonds in the lysine methyltransferase SET7/9
Q53647851	Direct path integral estimators for isotope fractionation ratios.
Q99605780	Discovery of Novel Hsp90 C-Terminal Inhibitors Using 3D-Pharmacophores Derived from Molecular Dynamics Simulations
Q64076594	Distinct Dopamine D₂ Receptor Antagonists Differentially Impact D₂ Receptor Oligomerization
Q92962714	Distinct inactive conformations of the dopamine D2 and D3 receptors correspond to different extents of inverse agonism
Q58692239	Do Better Quality Embedding Potentials Accelerate the Convergence of QM/MM Models? The Case of Solvated Acid Clusters
Q33924383	Do Halogen-Hydrogen Bond Donor Interactions Dominate the Favorable Contribution of Halogens to Ligand-Protein Binding?
Q40816321	Docking Studies and Molecular Dynamic Simulations Reveal Different Features of IDO1 Structure
Q92093878	Domain sliding of two Staphylococcus aureus N-acetylglucosaminidases enables their substrate-binding prior to its catalysis
Q89874907	Donepezil Inhibits Acetylcholinesterase via Multiple Binding Modes at Room Temperature
Q36082949	Drug search for leishmaniasis: a virtual screening approach by grid computing.
Q48188313	Drug-Drug Interactions between Atorvastatin and Dronedarone Mediated by Monomeric CYP3A4.
Q90332778	Drug-Triggered Self-Assembly of Linear Polymer into Nanoparticles for Simultaneous Delivery of Hydrophobic and Hydrophilic Drugs in Breast Cancer Cells
Q24633124	Druggability Assessment of Allosteric Proteins by Dynamics Simulations in the Presence of Probe Molecules
Q30375558	Dual Allosteric Inhibitors Jointly Modulate Protein Structure and Dynamics in the Hepatitis C Virus Polymerase.
Q35599256	Dual mechanism of ion permeation through VDAC revealed with inorganic phosphate ions and phosphate metabolites
Q34234550	Duplication of a promiscuous transcription factor drives the emergence of a new regulatory network
Q104567478	Dynamic 3D proteomes reveal protein functional alterations at high resolution in situ
Q43670417	Dynamic Conformational States Dictate Selectivity toward the Native Substrate in a Substrate-Permissive Acyltransferase
Q92423429	Dynamic Protonation Dramatically Affects the Membrane Permeability of Drug-like Molecules
Q41200379	Dynamic and Kinetic Elements of µ-Opioid Receptor Functional Selectivity
Q38264255	Effect of Terminal Groups of Dendrimers in the Complexation with Antisense Oligonucleotides and Cell Uptake.
Q34377784	Effect of magnesium on calcium and oxalate ion binding
Q35177027	Effect of membrane tension on the electric field and dipole potential of lipid bilayer membrane
Q47651833	Effect of single-residue bulges on RNA double-helical structures: crystallographic database analysis and molecular dynamics simulation studies.
Q90579367	Effects of Low-level Lipid Peroxidation on the Permeability of Nitroaromatic Molecules across a Membrane: A Computational Study
Q64098537	Effects of Selective Substitution of Cysteine Residues on the Conformational Properties of Chlorotoxin Explored by Molecular Dynamics Simulations
Q36627544	Effects of cytosine modifications on DNA flexibility and nucleosome mechanical stability
Q35812347	Efficient Exploration of Membrane-Associated Phenomena at Atomic Resolution
Q46731467	Efficient Strategy for the Calculation of Solvation Free Energies in Water and Chloroform at the Quantum Mechanical/Molecular Mechanical Level
Q43008057	Efficient conformational sampling and weak scoring in docking programs? Strategy of the wisdom of crowds.
Q62111621	Electro-Mechanical Conductance Modulation of a Nanopore Using a Removable Gate
Q88892909	Electronic absorption spectra of pyridine and nicotine in aqueous solution with a combined molecular dynamics and polarizable QM/MM approach
Q47767886	Electrostatic and induction effects in the solubility of water in alkanes.
Q34561303	Electrostatic channeling in P. falciparum DHFR-TS: Brownian dynamics and Smoluchowski modeling
Q90348471	Electrostatic lock in the transport cycle of the multidrug resistance transporter EmrE
Q92702850	Elucidating the Structural Basis of the Intracellular pH Sensing Mechanism of TASK-2 K2P Channels
Q98472951	Enantioseparation of mandelic acid on vancomycin column: Experimental and docking study
Q34568127	Enantiospecificity of chloroperoxidase-catalyzed epoxidation: biased molecular dynamics study of a cis-β-methylstyrene/chloroperoxidase-compound I complex
Q64901556	Energetic, Structural and Dynamic Properties of Nucleobase-Urea Interactions that Aid in Urea Assisted RNA Unfolding.
Q38619070	Energy-free machine learning force field for aluminum.
Q30636997	Equilibrated atomic models of outward-facing P-glycoprotein and effect of ATP binding on structural dynamics
Q41502311	Erythritol predicted to inhibit permeation of water and solutes through the conducting pore of P. falciparum aquaporin
Q27323050	Escherichia coli peptidoglycan structure and mechanics as predicted by atomic-scale simulations
Q36958036	Estimation of ligand efficacies of metabotropic glutamate receptors from conformational forces obtained from molecular dynamics simulations.
Q39248995	Estimation of relative free energies of binding using pre-computed ensembles based on the single-step free energy perturbation and the site-identification by Ligand competitive saturation approaches
Q38659321	Evaluating Force Field Performance in Thermodynamic Calculations of Cyclodextrin Host-Guest Binding: Water Models, Partial Charges, and Host Force Field Parameters
Q33893547	Evaluation of CM5 Charges for Condensed-Phase Modeling.
Q41846781	Evaluation of the novel algorithm of flexible ligand docking with moveable target-protein atoms
Q47959890	Evolution of Aggregate Structure in Solutions of Anionic Monorhamnolipids: Experimental and Computational Results.
Q90126004	Evolution of an amniote-specific mechanism for modulating ubiquitin signalling via phosphoregulation of the E2 enzyme UBE2D3
Q60959760	Evolution of cation binding in the active sites of P-loop nucleoside triphosphatases in relation to the basic catalytic mechanism
Q52331616	Examining the role of protein structural dynamics in drug resistance in Mycobacterium tuberculosis.
Q91668311	Experimentally guided computational antibody affinity maturation with de novo docking, modelling and rational design
Q58691660	Exploring Peptide⁻Solvent Interactions: A Computational Study
Q90733985	Exploring protein-protein interactions using the site-identification by ligand competitive saturation methodology
Q58743634	Exploring the Ligand Efficacy of Cannabinoid Receptor 1 (CB1) using Molecular Dynamics Simulations
Q47720710	Exploring the binding sites and binding mechanism for hydrotrope encapsulated griseofulvin drug on γ-tubulin protein
Q41108116	Exploring the binding sites and proton diffusion on insulin amyloid fibril surfaces by naphthol-based photoacid fluorescence and molecular simulations
Q37440194	Exploring the pH-dependent substrate transport mechanism of FocA using molecular dynamics simulation.
Q34347574	Extension of the CHARMM General Force Field to sulfonyl-containing compounds and its utility in biomolecular simulations.
Q30399172	Extension of the Highly Mobile Membrane Mimetic to Transmembrane Systems through Customized in Silico Solvents
Q51451305	Extracellular Loop 2 of the Adenosine A1 Receptor Has a Key Role in Orthosteric Ligand Affinity and Agonist Efficacy.
Q47745661	FRET monitoring of a nonribosomal peptide synthetase
Q28744012	Fatty acids derived from royal jelly are modulators of estrogen receptor functions
Q64259341	Fentanyl Family at the Mu-Opioid Receptor: Uniform Assessment of Binding and Computational Analysis
Q37337277	Fighting Cancer with Transition Metal Complexes: From Naked DNA to Protein and Chromatin Targeting Strategies
Q33784853	Filling up the heme pocket stabilizes apomyoglobin and speeds up its folding
Q38754277	Flexible CDOCKER: Development and application of a pseudo-explicit structure-based docking method within CHARMM
Q90620519	Flexible Fitting of Small Molecules into Electron Microscopy Maps Using Molecular Dynamics Simulations with Neural Network Potentials
Q30369353	Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel.
Q46372400	Fluorescence and NMR spectroscopy together with molecular simulations reveal amphiphilic characteristics of a Burkholderia biofilm exopolysaccharide
Q35661996	Force Field Benchmark of Organic Liquids: Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Isothermal Compressibility, Volumetric Expansion Coefficient, and Dielectric Constant
Q47616955	Force Field Parametrization of Metal Ions from Statistical Learning Techniques.
Q92515450	Force Fields for Small Molecules
Q47591502	Force field development and simulations of intrinsically disordered proteins
Q57057117	Force matching as a stepping stone to QM/MM CB[8] host/guest binding free energies: a SAMPL6 cautionary tale
Q41422778	Forces and Disease: Electrostatic force differences caused by mutations in kinesin motor domains can distinguish between disease-causing and non-disease-causing mutations.
Q41904585	Formation of β-cyclodextrin complexes in an anhydrous environment.
Q34222933	Fragment-based docking: development of the CHARMMing Web user interface as a platform for computer-aided drug design
Q91622583	Free Energy Calculations Based on Coupling Proximal Distribution Functions and Thermodynamic Cycles
Q37651766	Free energy landscape of G-protein coupled receptors, explored by accelerated molecular dynamics
Q52583323	Free energy simulations reveal molecular mechanism for functional switch of a DNA helicase.
Q36566354	Free energy surface of the Michaelis complex of lactate dehydrogenase: a network analysis of microsecond simulations
Q83327383	From sequence to 3D structure of hyperbranched molecules: application to surface modified PAMAM dendrimers
Q35124890	Functional mechanism of C-terminal tail in the enzymatic role of porcine testicular carbonyl reductase: a combined experiment and molecular dynamics simulation study of the C-terminal tail in the enzymatic role of PTCR.
Q90646236	G-Protein-Coupled Receptor-Membrane Interactions Depend on the Receptor Activation State
Q29615867	GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit
Q37734636	Gas-phase ion isomer analysis reveals the mechanism of peptide sequence scrambling.
Q49790548	Gi- and Gs-coupled GPCRs show different modes of G-protein binding.
Q47842925	Gibbs Sampler-Based λ-Dynamics and Rao-Blackwell Estimator for Alchemical Free Energy Calculation
Q30405636	Glycan Reader: automated sugar identification and simulation preparation for carbohydrates and glycoproteins
Q30403000	Gorge Motions of Acetylcholinesterase Revealed by Microsecond Molecular Dynamics Simulations
Q48323259	Graph-Theoretic Analysis of Monomethyl Phosphate Clustering in Ionic Solutions.
Q38979654	Heterogeneous dielectric generalized Born model with a van der Waals term provides improved association energetics of membrane-embedded transmembrane helices
Q95642450	High-Strength, Durable All-Silk Fibroin Hydrogels with Versatile Processability toward Multifunctional Applications
Q27675402	High-resolution crystal structure of human protease-activated receptor 1
Q100669110	High-resolution structures of multiple 5-HT3AR-setron complexes reveal a novel mechanism of competitive inhibition
Q91590854	Histidine at position 462 determines the low quinine sensitivity of ether-à-go-go channel superfamily member Kv 12.1.
Q35970217	How Far Does a Receptor Influence Vibrational Properties of an Odorant?
Q44340976	How Oliceridine (TRV-130) Binds and Stabilizes a μ-Opioid Receptor Conformational State That Selectively Triggers G Protein Signaling Pathways
Q89540527	How accurate are approximate quantum chemical methods at modelling solute-solvent interactions in solvated clusters?
Q42316572	Hsp90 dependence of a kinase is determined by its conformational landscape
Q91883298	Human CYP2E1-Dependent Mutagenicity of Benzene and Its Hydroxylated Metabolites in V79-derived cells: Suppression and Enhancement by Ethanol Pretreatment
Q39989280	Hybrid Steered Molecular Dynamics Approach to Computing Absolute Binding Free Energy of Ligand-Protein Complexes: A Brute Force Approach That Is Fast and Accurate
Q48417639	Hydration properties of natural and synthetic DNA sequences with methylated adenine or cytosine bases in the R.DpnI target and BDNF promoter studied by molecular dynamics simulations.
Q35282762	Hydrogen-bonded water molecules in the M2 channel of the influenza A virus guide the binding preferences of ammonium-based inhibitors
Q36701010	Hydroxymethyluracil modifications enhance the flexibility and hydrophilicity of double-stranded DNA.
Q58611387	Identification and Characterization of NTB451 as a Potential Inhibitor of Necroptosis
Q30362294	Identification and Characterization of Noncovalent Interactions That Drive Binding and Specificity in DD-Peptidases and β-Lactamases
Q48319926	Identification of Inhibitors Targeting Ferredoxin-NADP⁺ Reductase from the Xanthomonas citri subsp. citri Phytopathogenic Bacteria.
Q53698033	Identification of Serine 119 as an Effective Inhibitor Binding Site of M. tuberculosis Ubiquitin-like Protein Ligase PafA Using Purified Proteins and M. smegmatis.
Q58845447	Identification of Thiourea-Based Inhibitors of the B-Cell Lymphoma 6 BTB Domain via NMR-Based Fragment Screening and Computer-Aided Drug Design
Q47323511	Identification of Two New Cholesterol Interaction Sites on the A2A Adenosine Receptor
Q55690406	Identification of a New Function of Cardiovascular Disease Drug 3-Morpholinosydnonimine Hydrochloride as an Amyloid-β Aggregation Inhibitor.
Q89619971	Identification of a Selective PDE4B Inhibitor From Bryophyllum pinnatum by Target Fishing Study and In Vitro Evaluation of Quercetin 3-O-α-L-Arabinopyranosyl-(1→2)-O-α-L-Rhamnopyranoside
Q38383492	Identification of novel natural inhibitor for NorM - a multidrug and toxic compound extrusion transporter - an insilico molecular modeling and simulation studies
Q37367535	Iminoguanidines as Allosteric Inhibitors of the Iron-Regulated Heme Oxygenase (HemO) of Pseudomonas aeruginosa
Q90486936	Impact of electronic polarizability on protein-functional group interactions
Q28533868	Impact of ribosomal modification on the binding of the antibiotic telithromycin using a combined grand canonical monte carlo/molecular dynamics simulation approach
Q41438092	Impact of sterol tilt on membrane bending rigidity in cholesterol and 7DHC-containing DMPC membranes
Q36662426	Impact of substrate protonation and tautomerization states on interactions with the active site of arginase I.
Q40744576	Implication of Caspase-3 as a Common Therapeutic Target for Multineurodegenerative Disorders and Its Inhibition Using Nonpeptidyl Natural Compounds
Q92999523	Improved Modeling of Halogenated Ligand-Protein Interactions Using the Drude Polarizable and CHARMM Additive Empirical Force Fields
Q39342022	Improving the Force Field Description of Tyrosine-Choline Cation-π Interactions: QM Investigation of Phenol-N(Me)4+ Interactions
Q91746598	In Silico Design and Characterization of Graphene Oxide Membranes with Variable Water Content and Flake Oxygen Content
Q99634880	In Silico Finding of Key Interaction Mediated α3β4 and α7 Nicotinic Acetylcholine Receptor Ligand Selectivity of Quinuclidine-Triazole Chemotype
Q92187126	In Silico Screening of Aptamers Configuration against Hepatitis B Surface Antigen
Q89597711	In Silico Strategies in Tuberculosis Drug Discovery
Q28486185	In silico analysis of putative paralytic shellfish poisoning toxins export proteins in cyanobacteria
Q96954135	In silico simulations of erythrocyte aquaporins with quantitative in vitro validation
Q50675544	In silico study of the structurally similar ORL1 receptor agonist and antagonist pairs reveal possible mechanism of receptor activation.
Q30843053	In silico-based vaccine design against Ebola virus glycoprotein
Q30585632	In vivo structure-activity relationship studies support allosteric targeting of a dual specificity phosphatase
Q46745149	In-silico analysis of the structure and binding site features of an α-expansin protein from mountain papaya fruit (VpEXPA2), through molecular modeling, docking, and dynamics simulation studies
Q35045753	Inclusion of multiple fragment types in the site identification by ligand competitive saturation (SILCS) approach
Q36025678	Incorporation of charged residues in the CYP2J2 F-G loop disrupts CYP2J2-lipid bilayer interactions
Q47134184	Increasing vaccine production using pulsed ultrasound waves
Q89442663	Indexing of grazing-incidence X-ray diffraction patterns: the case of fibre-textured thin films
Q92932572	Influence of Hydration on the Structure of Reline Deep Eutectic Solvent: A Molecular Dynamics Study
Q28386865	Inhibition of Peroxidase Activity of Cytochrome c: De Novo Compound Discovery and Validation
Q92941611	Initial Studies Directed toward the Rational Design of Aqueous Graphene Dispersants
Q56335987	Inositol phosphates are assembly co-factors for HIV-1
Q60920862	Insight into Inhibitor Binding in the Eukaryotic Proteasome: Computations of the 20S CP
Q39361317	Insight into NSAID-induced membrane alterations, pathogenesis and therapeutics: characterization of interaction of NSAIDs with phosphatidylcholine.
Q90049722	Insights From Molecular Dynamics Simulations of a Number of G-Protein Coupled Receptor Targets for the Treatment of Pain and Opioid Use Disorders
Q52310258	Insights Into the Bifunctional Aphidicolan-16-ß-ol Synthase Through Rapid Biomolecular Modeling Approaches.
Q27676539	Insights into Diterpene Cyclization from Structure of Bifunctional Abietadiene Synthase from Abies grandis
Q49331890	Insights into Key Interactions between Vancomycin and Bacterial Cell Wall Structures.
Q55421031	Insights into molecular mechanisms of drug metabolism dysfunction of human CYP2C9*30.
Q40803358	Insights into the Modulation of Dopamine Transporter Function by Amphetamine, Orphenadrine, and Cocaine Binding
Q33811883	Insights into the binding mode of MEK type-III inhibitors. A step towards discovering and designing allosteric kinase inhibitors across the human kinome
Q57990988	Insights into the structural determinants for selective inhibition of nitric oxide synthase isoforms
Q88013425	Insulin adsorption on functionalized silica surfaces: an accelerated molecular dynamics study
Q91703582	Inter-Active Site Communication Mediated by the Dimer Interface β-Sheet in the Half-the-Sites Enzyme, Thymidylate Synthase
Q37627329	Interaction between functionalized gold nanoparticles in physiological saline
Q50216827	Interaction of Artepillin C with model membranes.
Q64277705	Interaction of SNARE Mimetic Peptides with Lipid bilayers: Effects of Secondary Structure, Bilayer Composition and Lipid Anchoring
Q96113366	Interaction of the prototypical α-ketoamide inhibitor with the SARS-CoV-2 main protease active site in silico: Molecular dynamic simulations highlight the stability of the ligand-protein complex
Q27316335	Interactions of L-3,5,3'-Triiodothyronine [corrected], Allopregnanolone, and Ivermectin with the GABAA Receptor: Evidence for Overlapping Intersubunit Binding Modes
Q35572367	Interactions of amino acid side-chain analogs within membrane environments
Q34074459	Interactions of protein kinase C-α C1A and C1B domains with membranes: a combined computational and experimental study
Q35687162	Interactions of the anticancer drug tamoxifen with lipid membranes
Q40100405	Interdomain salt-bridges in the Ebola virus protein VP40 and their role in domain association and plasma membrane localization
Q61799046	Interplay between lipid lateral diffusion, dye concentration and membrane permeability unveiled by a combined spectroscopic and computational study of a model lipid bilayer
Q35013441	Intramolecular charge-assisted hydrogen bond strength in pseudochair carboxyphosphate
Q112426270	Intuitive, reproducible high-throughput molecular dynamics in Galaxy: a tutorial
Q47132843	Investigating Small-Molecule Ligand Binding to G Protein-Coupled Receptors with Biased or Unbiased Molecular Dynamics Simulations
Q35676787	Ionic transport through sub-10 nm diameter hydrophobic high-aspect ratio nanopores: experiment, theory and simulation
Q50892902	Iron depletion strategy for targeted cancer therapy: utilizing the dual roles of neutrophil gelatinase-associated lipocalin protein.
Q36758886	Kainate receptor pore-forming and auxiliary subunits regulate channel block by a novel mechanism
Q41963460	Kirkwood-Buff analysis of aqueous N-methylacetamide and acetamide solutions modeled by the CHARMM additive and Drude polarizable force fields.
Q37701430	LIBSA--a method for the determination of ligand-binding preference to allosteric sites on receptor ensembles
Q92145328	LUF7244, an allosteric modulator/activator of Kv 11.1 channels, counteracts dofetilide-induced torsades de pointes arrhythmia in the chronic atrioventricular block dog model
Q90240287	Learning how planarization can affect dichroic patterns in polyfluorenes
Q35934124	Ligand-Induced Proton Transfer and Low-Barrier Hydrogen Bond Revealed by X-ray Crystallography
Q33998174	Ligand-dependent activation and deactivation of the human adenosine A(2A) receptor.
Q40647572	Ligand-dependent cholesterol interactions with the human A(2A) adenosine receptor
Q35001962	Ligand-modulated interactions between charged monolayer-protected Au144(SR)60 gold nanoparticles in physiological saline.
Q41283780	Limiting assumptions in molecular modeling: electrostatics
Q38302930	Lipid-linked oligosaccharides in membranes sample conformations that facilitate binding to oligosaccharyltransferase
Q89546391	Lipopolysaccharide Simulations Are Sensitive to Phosphate Charge and Ion Parameterization
Q99630282	LncRNA-SLC16A1-AS1 induces metabolic reprogramming during Bladder Cancer progression as target and co-activator of E2F1
Q34583479	Local anesthetic and antiepileptic drug access and binding to a bacterial voltage-gated sodium channel
Q93000767	Low-diluted Phenacetinum disrupted the melanoma cancer cell migration
Q34063434	MATCH: an atom-typing toolset for molecular mechanics force fields.
Q26799988	MD Simulations of tRNA and Aminoacyl-tRNA Synthetases: Dynamics, Folding, Binding, and Allostery
Q82599858	MM/GBSA and LIE estimates of host-guest affinities: dependence on charges and solvation model
Q45349630	Macrodomain-containing proteins are new mono-ADP-ribosylhydrolases.
Q35858545	Macromolecular Crystallography for Synthetic Abiological Molecules: Combining xMDFF and PHENIX for Structure Determination of Cyanostar Macrocycles
Q59801554	Main-chain mutagenesis reveals intrahelical coupling in an ion channel voltage-sensor
Q38818413	Mapping Ryanodine Binding Sites in the Pore Cavity of Ryanodine Receptors.
Q35818750	Mapping fast protein folding with multiple-site fluorescent probes
Q42110736	Mapping functional group free energy patterns at protein occluded sites: nuclear receptors and G-protein coupled receptors
Q35924198	Mass partitioning effects in diffusion transport
Q37119798	Matching of additive and polarizable force fields for multiscale condensed phase simulations
Q28082151	Mathematical and computational modeling in biology at multiple scales
Q35746284	Mechanism of Ion Permeation in Mammalian Voltage-Gated Sodium Channels
Q52579430	Mechanism of NMDA receptor channel block by MK-801 and memantine.
Q36590427	Mechanism of drug-drug interactions mediated by human cytochrome P450 CYP3A4 monomer
Q45938036	Mechanism of intracellular allosteric β2AR antagonist revealed by X-ray crystal structure.
Q34041202	Mechanistic insights into the allosteric modulation of opioid receptors by sodium ions
Q34467026	Membrane-induced structural rearrangement and identification of a novel membrane anchor in talin F2F3
Q89673230	Menthol Binding to the Human α4β2 Nicotinic Acetylcholine Receptor Facilitated by Its Strong Partitioning in the Membrane
Q60920652	Menthol Stereoisomers Exhibit Different Effects on α4β2 nAChR Upregulation and Dopamine Neuron Spontaneous Firing
Q91559489	Mesoscale reaction-diffusion phenomena governing lignin-first biomass fractionation
Q30363020	Metal Ion Modeling Using Classical Mechanics
Q64261276	Metal based donepezil analogues designed to inhibit human acetylcholinesterase for Alzheimer's disease
Q33919887	Methodology for the Simulation of Molecular Motors at Different Scales
Q90454303	Methylpiperidinium Iodides as Novel Antagonists for α7 Nicotinic Acetylcholine Receptors
Q51590304	Microscopic Characterization of Membrane Transporter Function by In Silico Modeling and Simulation.
Q47131761	Mineral surface chemistry control for origin of prebiotic peptides.
Q38933492	Mixed-Probe Simulation and Probe-Derived Surface Topography Map Analysis for Ligand Binding Site Identification.
Q38836142	Modeling Molecular Interactions in Water: From Pairwise to Many-Body Potential Energy Functions.
Q35987132	Modeling Protein-Ligand Binding by Mining Minima
Q89738038	Modified cyclodextrins as broad-spectrum antivirals
Q99546570	Modulating the tension-time integral of the cardiac twitch prevents dilated cardiomyopathy in murine hearts
Q54968538	Modulation of Hoogsteen dynamics on DNA recognition.
Q28548366	Molecular Determinants Underlying Binding Specificities of the ABL Kinase Inhibitors: Combining Alanine Scanning of Binding Hot Spots with Network Analysis of Residue Interactions and Coevolution
Q48020118	Molecular Dynamics Methodologies for Probing Cannabinoid Ligand/Receptor Interaction
Q64331808	Molecular Dynamics Simulation of the Oil Sequestration Properties of a Nonionic Rhamnolipid
Q92373168	Molecular Dynamics Simulations of Ionic Liquids and Electrolytes Using Polarizable Force Fields
Q98291777	Molecular Dynamics Simulations of Mite Aquaporin DerfAQP1 from the Dust Mite Dermatophagoides farinae (Acariformes: Pyroglyphidae)
Q64086965	Molecular Dynamics Simulations of the Allosteric Modulation of the Adenosine A2A Receptor by a Mini-G Protein
Q48043748	Molecular Mechanism of Resveratrol's Lipid Membrane Protection.
Q90903674	Molecular Mechanism of T-2 Toxin-Induced Cerebral Edema by Aquaporin-4 Blocking and Permeation
Q41821421	Molecular Simulations of Solved Co-crystallized X-Ray Structures Identify Action Mechanisms of PDEδ Inhibitors.
Q34018861	Molecular basis of ligand dissociation in β-adrenergic receptors
Q104495316	Molecular determinant of substrate binding and specificity of cytochrome P450 2J2
Q41882659	Molecular determinants of phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) binding to transient receptor potential V1 (TRPV1) channels
Q89143916	Molecular determination of claudin-15 organization and channel selectivity
Q35764364	Molecular docking based screening of novel designed chalcone series of compounds for their anti-cancer activity targeting EGFR kinase domain
Q94606251	Molecular dynamic simulations to investigate the structural impact of known drug resistance mutations on HIV-1C Integrase-Dolutegravir binding
Q34222040	Molecular dynamics analysis of apolipoprotein-D-lipid hydroperoxide interactions: mechanism for selective oxidation of Met-93.
Q42053263	Molecular dynamics of class A β-lactamases-effects of substrate binding
Q48184197	Molecular dynamics of conformation-specific dopamine transporter-inhibitor complexes
Q47954235	Molecular dynamics simulations and molecular flooding studies of the retinoid X-receptor ligand binding domain.
Q27304950	Molecular dynamics simulations of DNA-free and DNA-bound TAL effectors
Q35051302	Molecular dynamics simulations of DNA/PEI complexes: effect of PEI branching and protonation state
Q35957416	Molecular dynamics simulations of glycoproteins using CHARMM.
Q42577895	Molecular dynamics simulations on the effect of size and shape on the interactions between negative Au18(SR)14, Au102(SR)44 and Au144(SR)60 nanoparticles in physiological saline.
Q48355427	Molecular dynamics simulations reveal the conformational dynamics of Arabidopsis thaliana BRI1 and BAK1 receptor-like kinases.
Q28480662	Molecular dynamics simulations suggest ligand's binding to nicotinamidase/pyrazinamidase
Q34061826	Molecular dynamics study of binding of µ-conotoxin GIIIA to the voltage-gated sodium channel Na(v)1.4.
Q39731555	Molecular dynamics study of human carbonic anhydrase II in complex with Zn(2+) and acetazolamide on the basis of all-atom force field simulations
Q35623525	Molecular dynamics to enhance structure-based virtual screening on cathepsin B.
Q27012799	Molecular dynamics, monte carlo simulations, and langevin dynamics: a computational review
Q42111862	Molecular interactions of Alzheimer's biomarker FDDNP with Aβ peptide
Q38129103	Molecular mechanics
Q52803488	Molecular mechanism of GPCR-mediated arrestin activation.
Q92034587	Molecular mechanism of setron-mediated inhibition of full-length 5-HT3A receptor
Q81131476	Molecular modeling of nucleic acid structure: setup and analysis
Q27325455	Molecular modeling of the human P2Y14 receptor: A template for structure-based design of selective agonist ligands.
Q91940302	Molecular simulation studies on B-cell lymphoma/leukaemia 11A (BCL11A)
Q52567375	Molecular simulations of self-assembling bio-inspired supramolecular systems and their connection to experiments.
Q33939578	Molecular switch controlling the binding of anionic bile acid conjugates to human apical sodium-dependent bile acid transporter.
Q27302413	Molecular switches of the κ opioid receptor triggered by 6'-GNTI and 5'-GNTI.
Q26777242	Monoamine transporters: insights from molecular dynamics simulations
Q65555236	Monte Carlo simulation of mixed nonionic Brij surfactants in water
Q35572848	Multi-Site λ-dynamics for simulated Structure-Activity Relationship studies
Q37022352	Multi-kinase inhibitors can associate with heat shock proteins through their NH2-termini by which they suppress chaperone function
Q89724286	Multi-phase Boltzmann weighting: accounting for local inhomogeneity in molecular simulations of water-octanol partition coefficients in the SAMPL6 challenge
Q38175308	Multi-scale computational enzymology: enhancing our understanding of enzymatic catalysis
Q99585096	Multiple Reaction Pathways in the Morphinone Reductase-Catalyzed Hydride Transfer Reaction
Q35157925	Multiple environment single system quantum mechanical/molecular mechanical (MESS-QM/MM) calculations. 1. Estimation of polarization energies
Q37701502	Multiscale Free Energy Simulations: An Efficient Method for Connecting Classical MD Simulations to QM or QM/MM Free Energies Using Non-Boltzmann Bennett Reweighting Schemes
Q38736948	Multiscale Modeling in the Clinic: Drug Design and Development
Q36058098	Multiscale simulation of microbe structure and dynamics
Q30399333	Mutation of Tyr137 of the universal Escherichia coli fimbrial adhesin FimH relaxes the tyrosine gate prior to mannose binding
Q47940837	Nanopore Sensing of Protein Folding
Q38914037	Nanostructure and stability of calcitonin amyloids
Q90239410	Neutron and X-ray crystal structures of Lactobacillus brevis alcohol dehydrogenase reveal new insights into hydrogen-bonding pathways
Q58562449	New Insights into Quinine-DNA Binding Using Raman Spectroscopy and Molecular Dynamics Simulations
Q48051566	Nonpolar Solvation Free Energy from Proximal Distribution Functions
Q58696379	Novel Alkylimidazolium Ionic Liquids as an Antibacterial Alternative to Pathogens of the Skin and Soft Tissue Infections
Q37025051	Novel Analogues of (R)-5-(Methylamino)-5,6-dihydro-4H-imidazo[4,5,1-ij]quinolin-2(1H)-one (Sumanirole) Provide Clues to Dopamine D2/D3 Receptor Agonist Selectivity
Q58606245	Novel Molecular-Dynamics-Based Protocols for Phase Space Sampling in Complex Systems
Q42380665	Novel Noncatalytic Substrate-Selective p38α-Specific MAPK Inhibitors with Endothelial-Stabilizing and Anti-Inflammatory Activity.
Q37006985	Novel protein-inhibitor interactions in site 3 of Ca(2+)-bound S100B as discovered by X-ray crystallography
Q35906422	Numerical study on the partitioning of the molecular polarizability into fluctuating charge and induced atomic dipole contributions
Q90315221	Nα-acetylation of the virulence factor EsxA is required for mycobacterial cytosolic translocation and virulence
Q35228698	On calculation of the electrostatic potential of a phosphatidylinositol phosphate-containing phosphatidylcholine lipid membrane accounting for membrane dynamics
Q55421368	On the Difference Between Additive and Subtractive QM/MM Calculations.
Q50864015	On the accuracy of population analyses based on fitted densities.
Q90728209	On the convergence of multi-scale free energy simulations
Q38820111	On the permeation of large organic cations through the pore of ATP-gated P2X receptors.
Q35230802	OptMAVEn--a new framework for the de novo design of antibody variable region models targeting specific antigen epitopes
Q89906827	Optimization of a Benzothiazole Indolene Scaffold Targeting Bacterial Cell Wall Assembly
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P8978	DBLP publication ID	journals/jcc/VanommeslaegheHAKZSDGLVM10
P356	DOI	10.1002/JCC.21367
P3181	OpenCitations bibliographic resource ID	597581
P932	PMC publication ID	2888302
P698	PubMed publication ID	19575467
P5875	ResearchGate publication ID	26338955

P50	author	Alex MacKerell	Q57907659
		Kenno Vanommeslaeghe	Q38318385
P2093	author name string	S Zhong
		S Kundu
		C Acharya
		P Lopes
		J Shim
		I Vorobyov
		E Darian
		E Hatcher
		O Guvench
P2860	cites work	CHARMM: A program for macromolecular energy, minimization, and dynamics calculations	Q53340989
		New formulation for derivatives of torsion angles and improper torsion angles in molecular mechanics: Elimination of singularities	Q54152664
		A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules	Q55918670
		Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems	Q56750591
		Use of Oligodeoxyribonucleotides with Conformationally Constrained Abasic Sugar Targets To Probe the Mechanism of Base Flipping byHhaI DNA (Cytosine C5)-methyltransferase	Q56770513
		Additive and Classical Drude Polarizable Force Fields for Linear and Cyclic Ethers	Q58846304
		An ab Initio Study on the Torsional Surface of Alkanes and Its Effect on Molecular Simulations of Alkanes and a DPPC Bilayer	Q58846423
		Polarizable Empirical Force Field for Alkanes Based on the Classical Drude Oscillator Model	Q58846482
		An ab Initio Quantum Mechanical Study of Hydrogen-Bonded Complexes of Biological Interest	Q58846590
		Structural Characterization of the Phosphotyrosine Binding Region of a High-Affinity SH2 Domain−Phosphopeptide Complex by Molecular Dynamics Simulation and Chemical Shift Calculations	Q58846728
		Systematic ab initio gradient calculation of molecular geometries, force constants, and dipole moment derivatives	Q59211600
		A molecular dynamics method for simulations in the canonical ensemble	Q59541597
		Canonical dynamics: Equilibrium phase-space distributions	Q21709091
		CHARMM: the biomolecular simulation program	Q24658108
		Comparison of simple potential functions for simulating liquid water	Q26778447
		All-atom empirical potential for molecular modeling and dynamics studies of proteins	Q27860468
		Scalable molecular dynamics with NAMD	Q27860718
		The Amber biomolecular simulation programs	Q27860745
		Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94	Q28842789
		Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes	Q29397708
		Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations	Q29547631
		Development and testing of a general amber force field	Q29547642
		Automatic atom type and bond type perception in molecular mechanical calculations	Q29616744
		Simulating movement of tRNA into the ribosome during decoding	Q30476304
		Automated conformational energy fitting for force-field development.	Q33331891
		CHARMM Additive All-Atom Force Field for Acyclic Polyalcohols, Acyclic Carbohydrates and Inositol	Q33531677
		CHARMM Additive All-Atom Force Field for Glycosidic Linkages between Hexopyranoses	Q33531681
		Additive empirical force field for hexopyranose monosaccharides	Q33899141
		Intrinsic conformational energetics associated with the glycosyl torsion in DNA: a quantum mechanical study	Q34177467
		Empirical force fields for biological macromolecules: overview and issues.	Q34334583
		Ion selectivity in potassium channels	Q34547784
		Ab initio conformational analysis of nucleic acid components: intrinsic energetic contributions to nucleic acid structure and dynamics	Q34561394
		A computational study of nucleosomal DNA flexibility	Q35129020
		Ab initio modeling of glycosyl torsions and anomeric effects in a model carbohydrate: 2-ethoxy tetrahydropyran.	Q35881285
		Identification and characterization of small molecule inhibitors of the calcium-dependent S100B-p53 tumor suppressor interaction.	Q40509580
		Alcohols, ethers, carbohydrates, and related compounds. I. The MM4 force field for simple compounds	Q42603831
		Polyunsaturated fatty acids in lipid bilayers: intrinsic and environmental contributions to their unique physical properties.	Q43848421
		Combined ab initio/empirical approach for optimization of Lennard-Jones parameters for polar-neutral compounds	Q43940870
		Carbohydrate solution simulations: producing a force field with experimentally consistent primary alcohol rotational frequencies and populations	Q44124575
		2D conformationally sampled pharmacophore: a ligand-based pharmacophore to differentiate delta opioid agonists from antagonists.	Q44340649
		Improved treatment of the protein backbone in empirical force fields.	Q44735024
		Molecular recognition of aldehydes by aldehyde dehydrogenase and mechanism of nucleophile activation.	Q45076941
		Stereochemistry of nucleic acids and their constituents. XVIII. Conformational analysis of .alpha. nucleosides by x-ray crystallography	Q45080845
		Molecular-level organization of saturated and polyunsaturated fatty acids in a phosphatidylcholine bilayer containing cholesterol	Q45174823
		Pseudorotation motion in tetrahydrofuran: an ab initio study	Q46536509
		The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin	Q47682341
P433	issue	4
P407	language of work or name	English	Q1860
P921	main subject	CHARMM	Q902642
		force field	Q1341441
P304	page(s)	671-690
P577	publication date	2010-03-01
P1433	published in	Journal of Computational Chemistry	Q3186908
P1476	title	CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields
P478	volume	31

CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields

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