scholarly article | Q13442814 |
P8978 | DBLP publication ID | journals/jcamd/RizziMMYSGCIGMC18 |
P356 | DOI | 10.1007/S10822-018-0170-6 |
P2888 | exact match | https://scigraph.springernature.com/pub.10.1007/s10822-018-0170-6 |
P932 | PMC publication ID | 6301044 |
P698 | PubMed publication ID | 30415285 |
P50 | author | Wei Yao | Q87623763 |
Andrea Rizzi | Q89928272 | ||
Steven Murkli | Q92978222 | ||
John N McNeill | Q92978227 | ||
Matthew Sullivan | Q92978232 | ||
Lyle D Isaacs | Q47923335 | ||
David L. Mobley | Q55143475 | ||
Michael K Gilson | Q59820693 | ||
Bruce C. Gibb | Q68686623 | ||
John D. Chodera | Q41044041 | ||
P2093 | author name string | Michael W Chiu | |
P2860 | cites work | ORAC: a molecular dynamics simulation program to explore free energy surfaces in biomolecular systems at the atomistic level | Q84708455 |
Prediction of SAMPL4 host-guest binding affinities using funnel metadynamics | Q87307951 | ||
Free-energy perturbation and quantum mechanical study of SAMPL4 octa-acid host-guest binding energies | Q87611444 | ||
Synthesis of Water-Soluble Deep-Cavity Cavitands | Q88079880 | ||
Bind3P: Optimization of a Water Model Based on Host-Guest Binding Data | Q89009711 | ||
CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields | Q24632987 | ||
Blind prediction of HIV integrase binding from the SAMPL4 challenge | Q26864619 | ||
Rescoring Docking Hit Lists for Model Cavity Sites: Predictions and Experimental Testing | Q27649874 | ||
Chasing protons: how isothermal titration calorimetry, mutagenesis, and pKa calculations trace the locus of charge in ligand binding to a tRNA-binding enzyme | Q27690788 | ||
Integrated Modeling Program, Applied Chemical Theory (IMPACT) | Q28751619 | ||
Predictions of Ligand Selectivity from Absolute Binding Free Energy Calculations | Q28818600 | ||
Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew | Q29396077 | ||
Development and testing of a general amber force field | Q29547642 | ||
A hierarchical approach to all-atom protein loop prediction | Q29615859 | ||
Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation | Q29617869 | ||
Long-timescale molecular dynamics simulations of protein structure and function. | Q30376113 | ||
FRED pose prediction and virtual screening accuracy | Q30399715 | ||
The VSGB 2.0 model: a next generation energy model for high resolution protein structure modeling | Q30406909 | ||
Statistically optimal analysis of samples from multiple equilibrium states | Q30438437 | ||
Conformer generation with OMEGA: algorithm and validation using high quality structures from the Protein Databank and Cambridge Structural Database | Q30494222 | ||
Current status of the AMOEBA polarizable force field | Q30495924 | ||
Computational Calorimetry: High-Precision Calculation of Host-Guest Binding Thermodynamics | Q30670127 | ||
Efficient and Minimal Method to Bias Molecular Simulations with Experimental Data | Q31026843 | ||
Tracing changes in protonation: a prerequisite to factorize thermodynamic data of inhibitor binding to aldose reductase | Q33300883 | ||
Binding of cyclic carboxylates to octa-acid deep-cavity cavitand | Q33599960 | ||
Statistics and physical origins of pK and ionization state changes upon protein-ligand binding | Q33696041 | ||
The SAMPL4 host-guest blind prediction challenge: an overview. | Q33740864 | ||
The AGBNP2 Implicit Solvation Model. | Q33803629 | ||
Anion binding to hydrophobic concavity is central to the salting-in effects of Hofmeister chaotropes | Q33882768 | ||
The statistical-thermodynamic basis for computation of binding affinities: a critical review | Q33915676 | ||
Replica exchange with solute tempering: a method for sampling biological systems in explicit water | Q34048139 | ||
Prediction of SAMPL3 host-guest binding affinities: evaluating the accuracy of generalized force-fields | Q34249481 | ||
Blind prediction of host-guest binding affinities: a new SAMPL3 challenge. | Q34257034 | ||
Blind prediction of solvation free energies from the SAMPL4 challenge. | Q34409381 | ||
Accurate and reliable prediction of relative ligand binding potency in prospective drug discovery by way of a modern free-energy calculation protocol and force field | Q34459931 | ||
The cucurbit[n]uril family: prime components for self-sorting systems. | Q34466152 | ||
Relative Binding Free Energy Calculations in Drug Discovery: Recent Advances and Practical Considerations | Q47291097 | ||
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. | Q47567527 | ||
Prospective Evaluation of Free Energy Calculations for the Prioritization of Cathepsin L Inhibitors. | Q48045269 | ||
A combined treatment of hydration and dynamical effects for the modeling of host-guest binding thermodynamics: the SAMPL5 blinded challenge. | Q48054359 | ||
Millisecond dynamics of BTK reveal kinome-wide conformational plasticity within the apo kinase domain. | Q48296795 | ||
I. Dissociation free energies of drug-receptor systems via non-equilibrium alchemical simulations: a theoretical framework. | Q50643424 | ||
The SAMPL2 blind prediction challenge: introduction and overview. | Q51145300 | ||
FRED and HYBRID docking performance on standardized datasets. | Q51358561 | ||
The Role of the Active Site Flap in Streptavidin/Biotin Complex Formation. | Q52334871 | ||
On the Role of the Crystal Environment in Determining Protein Side-chain Conformations | Q58043852 | ||
A Blind Challenge for Computational Solvation Free Energies: Introduction and Overview | Q59795439 | ||
SAMPL3: blinded prediction of host–guest binding affinities, hydration free energies, and trypsin inhibitors | Q59795479 | ||
Equilibrium Free Energies from Nonequilibrium Measurements Using Maximum-Likelihood Methods | Q79283802 | ||
Climbing the Density Functional Ladder: Nonempirical Meta–Generalized Gradient Approximation Designed for Molecules and Solids | Q79283906 | ||
Protonation changes upon ligand binding to trypsin and thrombin: structural interpretation based on pK(a) calculations and ITC experiments | Q79815905 | ||
Well-defined, organic nanoenvironments in water: the hydrophobic effect drives a capsular assembly | Q80562577 | ||
A universal trend of amino acid gain and loss in protein evolution | Q81296862 | ||
Epik: a software program for pK( a ) prediction and protonation state generation for drug-like molecules | Q81360455 | ||
Water inside a hydrophobic cavitand molecule | Q81708786 | ||
Nonmonotonic assembly of a deep-cavity cavitand | Q83604855 | ||
The SAMPL3 blind prediction challenge: transfer energy overview | Q83811405 | ||
SAMPL2 challenge: prediction of solvation energies and tautomer ratios | Q84121860 | ||
Blind prediction of cyclohexane-water distribution coefficients from the SAMPL5 challenge | Q34541312 | ||
Acyclic cucurbit[n]uril-type molecular containers: influence of aromatic walls on their function as solubilizing excipients for insoluble drugs | Q34631587 | ||
New ultrahigh affinity host-guest complexes of cucurbit[7]uril with bicyclo[2.2.2]octane and adamantane guests: thermodynamic analysis and evaluation of M2 affinity calculations | Q34731466 | ||
KECSA-Movable Type Implicit Solvation Model (KMTISM). | Q35076388 | ||
OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins | Q35846188 | ||
Toward Improved Force-Field Accuracy through Sensitivity Analysis of Host-Guest Binding Thermodynamics | Q36331553 | ||
On the Role of Dewetting Transitions in Host-Guest Binding Free Energy Calculations. | Q36523088 | ||
A synthetic host-guest system achieves avidin-biotin affinity by overcoming enthalpy-entropy compensation | Q36696316 | ||
Computational scheme for pH-dependent binding free energy calculation with explicit solvent | Q36749493 | ||
Host-guest complexes with protein-ligand-like affinities: computational analysis and design | Q37343448 | ||
Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways | Q37582165 | ||
Binding free energies in the SAMPL5 octa-acid host-guest challenge calculated with DFT-D3 and CCSD(T). | Q37588656 | ||
Resolving the problem of trapped water in binding cavities: prediction of host-guest binding free energies in the SAMPL5 challenge by funnel metadynamics. | Q37588671 | ||
Advancing Drug Discovery through Enhanced Free Energy Calculations | Q38662672 | ||
Overview of the SAMPL5 host-guest challenge: Are we doing better? | Q38818618 | ||
On the fly estimation of host-guest binding free energies using the movable type method: participation in the SAMPL5 blind challenge | Q38971591 | ||
Accelerating drug discovery through tight integration of expert molecular design and predictive scoring | Q38999881 | ||
Predicting Binding Free Energies: Frontiers and Benchmarks | Q39235195 | ||
A Critical Review of Validation, Blind Testing, and Real-World Use of Alchemical Protein-Ligand Binding Free Energy Calculations | Q39245671 | ||
Blinded predictions of host-guest standard free energies of binding in the SAMPL5 challenge | Q39509919 | ||
Predicting small-molecule solvation free energies: an informal blind test for computational chemistry | Q40131892 | ||
Semiempirical Quantum Chemical PM6 Method Augmented by Dispersion and H-Bonding Correction Terms Reliably Describes Various Types of Noncovalent Complexes | Q40271952 | ||
Blind prediction of SAMPL4 cucurbit[7]uril binding affinities with the mining minima method | Q40579705 | ||
OpenMM 7: Rapid development of high performance algorithms for molecular dynamics. | Q41327186 | ||
Binding Hydrated Anions with Hydrophobic Pockets | Q41521132 | ||
Binding of carboxylate and trimethylammonium salts to octa-acid and TEMOA deep-cavity cavitands | Q41521138 | ||
The Movable Type Method Applied to Protein-Ligand Binding | Q41852852 | ||
Development of the knowledge-based and empirical combined scoring algorithm (KECSA) to score protein-ligand interactions | Q42062076 | ||
On the use of orientational restraints and symmetry corrections in alchemical free energy calculations | Q42106721 | ||
Evaluation of linked protonation effects in protein binding reactions using isothermal titration calorimetry | Q42108509 | ||
Acyclic cucurbit[n]uril congeners are high affinity hosts | Q43029591 | ||
A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu | Q43084146 | ||
Who cares for the protons? | Q43510076 | ||
Salt effects on the apparent stability of the cucurbit[7]uril-methyl viologen inclusion complex | Q44763293 | ||
SAMPL4, a blind challenge for computational solvation free energies: the compounds considered | Q45204541 | ||
Calculating binding free energies of host-guest systems using the AMOEBA polarizable force field | Q45710657 | ||
Towards the comprehensive, rapid, and accurate prediction of the favorable tautomeric states of drug-like molecules in aqueous solution. | Q45940902 | ||
II. Dissociation free energies in drug-receptor systems via nonequilibrium alchemical simulations: application to the FK506-related immunophilin ligands. | Q46546512 | ||
Determination of protein structures consistent with NMR order parameters | Q47270323 | ||
P433 | issue | 10 | |
P407 | language of work or name | English | Q1860 |
P921 | main subject | cucurbit[8]uril | Q27122603 |
P304 | page(s) | 937-963 | |
P577 | publication date | 2018-10-01 | |
P1433 | published in | Journal of Computer - Aided Molecular Design | Q15766522 |
P1476 | title | Overview of the SAMPL6 host-guest binding affinity prediction challenge | |
P478 | volume | 32 |
Q90654126 | Binding Thermodynamics of Host-Guest Systems with SMIRNOFF99Frosst 1.0.5 from the Open Force Field Initiative |
Q57057117 | Force matching as a stepping stone to QM/MM CB[8] host/guest binding free energies: a SAMPL6 cautionary tale |
Q99637403 | MMGB/SA Consensus Estimate of the Binding Free Energy Between the Novel Coronavirus Spike Protein to the Human ACE2 Receptor |
Q89724286 | Multi-phase Boltzmann weighting: accounting for local inhomogeneity in molecular simulations of water-octanol partition coefficients in the SAMPL6 challenge |
Q90012518 | New Trends in Virtual Screening |
Q56342046 | SAMPL6 host-guest blind predictions using a non equilibrium alchemical approach |
Q89460093 | SAMPL6 logP challenge: machine learning and quantum mechanical approaches |
Q97425970 | Upgraded AMBER Force Field for Zinc-Binding Residues and Ligands for Predicting Structural Properties and Binding Affinities in Zinc-Proteins |
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