CHARMM-GUI PDB manipulator for advanced modeling and simulations of proteins containing nonstandard residues.

scientific article published on 24 August 2014

CHARMM-GUI PDB manipulator for advanced modeling and simulations of proteins containing nonstandard residues. is …
instance of (P31):
review articleQ7318358
scholarly articleQ13442814

External links are
P356DOI10.1016/BS.APCSB.2014.06.002
P932PMC publication ID4739825
P698PubMed publication ID25443960

P50authorKenno VanommeslaegheQ38318385
Alex MacKerellQ57907659
P2093author name stringXi Cheng
Wei Han
Benoît Roux
Sunhwan Jo
Wonpil Im
Yifei Qi
Lei Huang
Hui Sun Lee
Huan Rui
Shahidul M Islam
Allen Zhu
P2860cites workOpen Babel: An open chemical toolboxQ21198766
Design of a Novel Globular Protein Fold with Atomic-Level AccuracyQ22242282
The RCSB Protein Data Bank: redesigned web site and web servicesQ24616175
CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fieldsQ24632987
CHARMM: the biomolecular simulation programQ24658108
SwissParam: A fast force field generation tool for small organic moleculesQ27136894
Structural determinants of nitroxide motion in spin-labeled proteins: Tertiary contact and solvent-inaccessible sites in helix G of T4 lysozymeQ27644663
Asymmetry in the structure of the ABC transporter-binding protein complex BtuCD-BtuFQ27646943
Structural determinants of nitroxide motion in spin-labeled proteins: Solvent-exposed sites in helix B of T4 lysozymeQ27649381
Structural origin of weakly ordered nitroxide motion in spin-labeled proteinsQ27655050
PRODRG: a tool for high-throughput crystallography of protein-ligand complexesQ27860633
Recovery from slow inactivation in K+ channels is controlled by water moleculesQ37237569
CHARMM-GUI Membrane Builder for mixed bilayers and its application to yeast membranesQ37263413
Chemoselective ligation and modification strategies for peptides and proteins.Q37346260
Multifrequency electron spin resonance spectra of a spin-labeled protein calculated from molecular dynamics simulationsQ37391160
Rapid parameterization of small molecules using the Force Field ToolkitQ37417543
Dynamics transitions at the outer vestibule of the KcsA potassium channel during gating.Q37571365
Unnatural amino acids as probes of ligand-receptor interactions and their conformational consequences.Q38072101
GRIFFIN: A versatile methodology for optimization of protein-lipid interfaces for membrane protein simulations.Q38589483
CHARMM-GUI PACE CG Builder for solution, micelle, and bilayer coarse-grained simulationsQ38739708
Application of binding free energy calculations to prediction of binding modes and affinities of MDM2 and MDMX inhibitorsQ39597289
Molecular basis of NMDA receptor-coupled ion channel modulation by S-nitrosylationQ40910444
Watching proteins move using site-directed spin labelingQ40933370
All-atom polarizable force field for DNA based on the classical Drude oscillator modelQ41512422
Motion of spin-labeled side chains in T4 lysozyme: effect of side chain structureQ41612776
Parametrization, molecular dynamics simulation, and calculation of electron spin resonance spectra of a nitroxide spin label on a polyalanine alpha-helixQ41948351
Contributions of counter-charge in a potassium channel voltage-sensor domain.Q42023842
Automation of the CHARMM General Force Field (CGenFF) II: assignment of bonded parameters and partial atomic charges.Q42184293
Automation of the CHARMM General Force Field (CGenFF) I: bond perception and atom typing.Q42199119
Impact of 2'-hydroxyl sampling on the conformational properties of RNA: update of the CHARMM all-atom additive force field for RNA.Q42226830
Alcohols, ethers, carbohydrates, and related compounds. I. The MM4 force field for simple compoundsQ42603831
LIPID11: a modular framework for lipid simulations using amberQ42607310
Reactivity of small thiolate anions and cysteine-25 in papain toward methyl methanethiosulfonateQ43487689
DEER distance measurements on proteinsQ43666647
MemBuilder: a web-based graphical interface to build heterogeneously mixed membrane bilayers for the GROMACS biomolecular simulation program.Q47827245
Energetics of ion conduction through the K+ channel.Q48620522
The cavity and pore helices in the KcsA K+ channel: electrostatic stabilization of monovalent cations.Q52210321
LAMBADA and InflateGRO2: efficient membrane alignment and insertion of membrane proteins for molecular dynamics simulations.Q54327591
A novel reversible thiol-specific spin label: Papain active site labeling and inhibitionQ72928315
External cysteine residues in the serotonin transporterQ73139649
CHARMM-GUI: a web-based graphical user interface for CHARMMQ80900573
An expanded eukaryotic genetic codeQ28201981
Adding new chemistries to the genetic codeQ28277278
The art and practice of structure-based drug design: A molecular modeling perspectiveQ29029768
Development and testing of a general amber force fieldQ29547642
Update of the CHARMM all-atom additive force field for lipids: validation on six lipid typesQ29616710
Automatic atom type and bond type perception in molecular mechanical calculationsQ29616744
Web interface for Brownian dynamics simulation of ion transport and its applications to beta-barrel poresQ30155430
Crystal structures of spin labeled T4 lysozyme mutants: implications for the interpretation of EPR spectra in terms of structure.Q30327038
CHARMM-GUI micelle builder for pure/mixed micelle and protein/micelle complex systems.Q30352184
Force Field for Peptides and Proteins based on the Classical Drude OscillatorQ30358273
A general method for site-specific incorporation of unnatural amino acids into proteins.Q30380652
WIWS: a protein structure bioinformatics Web service collectionQ30389657
Glycan Reader: automated sugar identification and simulation preparation for carbohydrates and glycoproteinsQ30405636
Three-dimensional architecture and gating mechanism of a K+ channel studied by EPR spectroscopyQ30472195
Structural refinement from restrained-ensemble simulations based on EPR/DEER data: application to T4 lysozymeQ30603705
Automated builder and database of protein/membrane complexes for molecular dynamics simulationsQ33298604
Simulations of the role of water in the protein-folding mechanismQ33694936
Conformational dynamics of ligand-dependent alternating access in LeuT.Q33729757
Additive empirical force field for hexopyranose monosaccharidesQ33899141
MATCH: an atom-typing toolset for molecular mechanics force fields.Q34063434
Biomolecular simulation: a computational microscope for molecular biologyQ34266180
Empirical force fields for biological macromolecules: overview and issues.Q34334583
The GROMOS software for biomolecular simulation: GROMOS05.Q34457783
Assessing the quality of absolute hydration free energies among CHARMM-compatible ligand parameterization schemesQ34537730
Design of functional metalloproteinsQ34659023
AUTOMATED FORCE FIELD PARAMETERIZATION FOR NON-POLARIZABLE AND POLARIZABLE ATOMIC MODELS BASED ON AB INITIO TARGET DATAQ35040558
Structure and dynamics of a conformationally constrained nitroxide side chain and applications in EPR spectroscopyQ35239853
Activation pathway of Src kinase reveals intermediate states as targets for drug designQ35738216
How does voltage open an ion channel?Q36480474
Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ(1) and χ(2) dihedral anglesQ36546184
CHARMM-GUI Ligand Binder for absolute binding free energy calculations and its applicationQ36569443
Cysteine substitution mutagenesis and the effects of methanethiosulfonate reagents at P2X2 and P2X4 receptors support a core common mode of ATP action at P2X receptors.Q36761837
Mechanism for alternating access in neurotransmitter transportersQ36785076
Restrained-ensemble molecular dynamics simulations based on distance histograms from double electron-electron resonance spectroscopyQ36933157
CHARMMing: a new, flexible web portal for CHARMM.Q37176721
P921main subjectCHARMMQ902642
P304page(s)235-265
P577publication date2014-08-24
P1433published inAdvances in protein chemistry and structural biologyQ26841838
P1476titleCHARMM-GUI PDB manipulator for advanced modeling and simulations of proteins containing nonstandard residues
P478volume96

Reverse relations

cites work (P2860)
Q98281056A computational structural study on the DNA-protecting role of the tardigrade-unique Dsup protein
Q42150684A novel proton transfer mechanism in the SLC11 family of divalent metal ion transporters
Q42375557Atomic mutagenesis in ion channels with engineered stoichiometry
Q38793733CHARMM-GUI 10 years for biomolecular modeling and simulation
Q36309757CHARMM-GUI HMMM Builder for Membrane Simulations with the Highly Mobile Membrane-Mimetic Model
Q30396234CHARMM-GUI MDFF/xMDFF Utilizer for Molecular Dynamics Flexible Fitting Simulations in Various Environments
Q48061728CHARMM-GUI ligand reader and modeler for CHARMM force field generation of small molecules
Q89770116Comprehensive structure-function analysis of causative variants in retinal pigment epithelium specific 65 kDa protein associated Leber Congenital Amaurosis
Q90814297Dynamic plasticity of the lipid antigen-binding site of CD1d is crucially favoured by acidic pH and helper proteins
Q39333078Effects of Spin-Labels on Membrane Burial Depth of MARCKS-ED Residues
Q90126004Evolution of an amniote-specific mechanism for modulating ubiquitin signalling via phosphoregulation of the E2 enzyme UBE2D3
Q58758683FIH permits NAA10 to catalyze the oxygen-dependent lysyl-acetylation of HIF-1α
Q49935761From a highly-disordered to a metastable state: Uncovering insights of α-synuclein.
Q33459363Glycan Reader is Improved to Recognize Most Sugar Types and Chemical Modifications in the Protein Data Bank.
Q38644272Identification of two natural compound inhibitors of Leishmania donovani Spermidine Synthase (SpdS) through molecular docking and dynamic studies
Q64103394L amino acid transporter structure and molecular bases for the asymmetry of substrate interaction
Q90063808Mapping of Ion and Substrate Binding Sites in Human Sodium Iodide Symporter (hNIS)
Q96223358Modeling and Simulation of a Fully-glycosylated Full-length SARS-CoV-2 Spike Protein in a Viral Membrane
Q30382622Molecular dynamics simulation strategies for protein-micelle complexes.
Q58082604ORAI1 channel gating and selectivity is differentially altered by natural mutations in the first or third transmembrane domain
Q47191286Relationship between lignocellulosic biomass dissolution and physicochemical properties of ionic liquids composed of 3-methylimidazolium cations and carboxylate anions
Q27704565Replacing Arginine 33 for Alanine in the Hemophore HasA from Pseudomonas aeruginosa Causes Closure of the H32 Loop in the Apo-Protein
Q89992782Site-Specific Peptide Probes Detect Buried Water in a Lipid Membrane
Q52688595Structural Dynamics of DPP-4 and Its Influence on the Projection of Bioactive Ligands.
Q64246916Synthesis, Biological Evaluation, and Molecular Modeling Studies of New Thiadiazole Derivatives as Potent P2X7 Receptor Inhibitors
Q57874015The molecular recognition of phosphatidic acid by an amphipathic helix in Opi1
Q58738012Two distinct conformations of factor H regulate discrete complement-binding functions in the fluid phase and at cell surfaces
Q97086757Virtual screening of approved drugs as potential SARS-CoV-2 main protease inhibitors

Search more.