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The key role of atom types, reference states, and interaction cutoff radii in the knowledge‐based method: New variational approach
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1002/(sici)1096-987x(199908)20:11<1165::aid-jcc7>3.0.co;2-aopenalex-snapshot
BLEEP?potential of mean force describing protein-ligand interactions: I. Generating potential
inferredcites →https://doi.org/10.1002/(sici)1096-987x(200003)21:4<295::aid-jcc5>3.0.co;2-8openalex-snapshot
Comparison of generalized born and poisson models: Energetics and dynamics of HIV protease
inferredcites →https://doi.org/10.1002/1521-3773(20020802)41:15<2644::aid-anie2644>3.0.co;2-oopenalex-snapshot
Approaches to the Description and Prediction of the Binding Affinity of Small-Molecule Ligands to Macromolecular Receptors
inferredcites →https://doi.org/10.1002/jcc.10112openalex-snapshot
Can the calculation of ligand binding free energies be improved with continuum solvent electrostatics and an ideal‐gas entropy correction?
inferredcites →https://doi.org/10.1002/pro.5560040923openalex-snapshot
A preference-based free-energy parameterization of enzyme-inhibitor binding. Applications to HIV-1-protease inhibitor design
inferredcites →https://doi.org/10.1002/prot.340230204openalex-snapshot
Why do protein architectures have boltzmann‐like statistics?
inferredcites →https://doi.org/10.1006/jmbi.1996.0868openalex-snapshot
Novel knowledge-based mean force potential at atomic level
inferredcites →https://doi.org/10.1006/jmbi.1999.3371openalex-snapshot
Knowledge-based scoring function to predict protein-ligand interactions
inferredcites →https://doi.org/10.1006/jmbi.2000.4285openalex-snapshot
Binding free energies and free energy components from molecular dynamics and Poisson-Boltzmann calculations. Application to amino acid recognition by aspartyl-tRNA synthetase11Edited by A. R. Fersht
inferredcites →https://doi.org/10.1006/jmbi.2001.4906openalex-snapshot
Four-body potentials reveal protein-specific correlations to stability changes caused by hydrophobic core mutations
inferredcites →https://doi.org/10.1007/bf00126743openalex-snapshot
The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure
inferredcites →https://doi.org/10.1007/s008940050096openalex-snapshot
SCORE: A New Empirical Method for Estimating the Binding Affinity of a Protein-Ligand Complex
inferredcites →https://doi.org/10.1016/0016-0032(57)90954-7openalex-snapshot
Statistical mechanics. Principles and selected applications
inferredcites →https://doi.org/10.1016/0022-2836(92)90693-eopenalex-snapshot
Topology fingerprint approach to the inverse protein folding problem
inferredcites →https://doi.org/10.1016/s0006-291x(03)00760-5openalex-snapshot
Comprehensive mutagenesis of HIV-1 protease: a computational geometry approach
inferredcites →https://doi.org/10.1016/s0022-2836(05)80269-4openalex-snapshot
Calculation of conformational ensembles from potentials of mena force
inferredcites →https://doi.org/10.1021/ci00009a001openalex-snapshot
Automatic assignment of chemical connectivity to organic molecules in the Cambridge Structural Database
inferredcites →https://doi.org/10.1021/ci9603487openalex-snapshot
BALI: Automatic Assignment of Bond and Atom Types for Protein Ligands in the Brookhaven Protein Databank
inferredcites →https://doi.org/10.1021/cr00023a004openalex-snapshot
Free energy calculations: Applications to chemical and biochemical phenomena
inferredcites →https://doi.org/10.1021/ja00172a038openalex-snapshot
Semianalytical treatment of solvation for molecular mechanics and dynamics
inferredcites →https://doi.org/10.1021/ja9539002openalex-snapshot
VALIDATE: A New Method for the Receptor-Based Prediction of Binding Affinities of Novel Ligands
inferredcites →https://doi.org/10.1021/ja963568+openalex-snapshot
Inclusion of Loss of Translational and Rotational Freedom in Theoretical Estimates of Free Energies of Binding. Application to a Complex of Benzene and Mutant T4 Lysozyme
inferredcites →https://doi.org/10.1021/jm000241hopenalex-snapshot
Binding of a Diverse Set of Ligands to Avidin and Streptavidin: An Accurate Quantitative Prediction of Their Relative Affinities by a Combination of Molecular Mechanics and Continuum Solvent Models
inferredcites →https://doi.org/10.1021/jm0105833openalex-snapshot
SMall Molecule Growth 2001 (SMoG2001): An Improved Knowledge-Based Scoring Function for Protein−Ligand Interactions
inferredcites →https://doi.org/10.1021/jm980536jopenalex-snapshot
A General and Fast Scoring Function for Protein−Ligand Interactions: A Simplified Potential Approach
inferredcites →https://doi.org/10.1021/jp961992ropenalex-snapshot
The GB/SA Continuum Model for Solvation. A Fast Analytical Method for the Calculation of Approximate Born Radii
inferredcites →https://doi.org/10.1021/ma00145a039openalex-snapshot
Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation
inferredcites →https://doi.org/10.1021/ma60054a013openalex-snapshot
Medium- and Long-Range Interaction Parameters between Amino Acids for Predicting Three-Dimensional Structures of Proteins
inferredcites →https://doi.org/10.1023/a:1007996124545openalex-snapshot
Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes
inferredcites →https://doi.org/10.1023/a:1008729005958openalex-snapshot
A knowledge-based scoring function for protein-ligand interactions: Probing the reference state
inferredcites →https://doi.org/10.1063/1.1353552openalex-snapshot
A “fast growth” method of computing free energy differences
inferredcites →https://doi.org/10.1073/pnas.162365999openalex-snapshot
On the calculation of absolute macromolecular binding free energies
inferredcites →https://doi.org/10.1093/protein/10.8.865openalex-snapshot
Residue-residue mean-force potentials for protein structure recognition
inferredcites →https://doi.org/10.1093/protein/8.7.677openalex-snapshot
Empirical free energy calculations of ligand-protein crystallographic complexes. I. Knowledge-based ligand-protein interaction potentials applied to the prediction of human immunodeficiency virus 1 protease binding affinity
inferredcites →https://doi.org/10.1146/annurev.biophys.30.1.211openalex-snapshot
Biomolecular Simulations: Recent Developments in Force Fields, Simulations of Enzyme Catalysis, Protein-Ligand, Protein-Protein, and Protein-Nucleic Acid Noncovalent Interactions
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1002/jcc.20246openalex-snapshot
New and fast statistical‐thermodynamic method for computation of protein‐ligand binding entropy substantially improves docking accuracy
inferred← citeshttps://doi.org/10.1002/prot.20673openalex-snapshot
Novel statistical‐thermodynamic methods to predict protein‐ligand binding positions using probability distribution functions
inferred← citeshttps://doi.org/10.1002/prot.21115openalex-snapshot
Structural analysis and prediction of protein mutant stability using distance and torsion potentials: Role of secondary structure and solvent accessibility
inferred← citeshttps://doi.org/10.1002/prot.21644openalex-snapshot
Interaction cutoff effect on ruggedness of protein–protein energy landscape
inferred← citeshttps://doi.org/10.1007/s10822-007-9116-0openalex-snapshot
Calculations of protein-ligand binding entropy of relative and overall molecular motions
inferred← citeshttps://doi.org/10.1021/acs.jctc.6b00090openalex-snapshot
An Atomistic Statistically Effective Energy Function for Computational Protein Design
inferred← citeshttps://doi.org/10.1021/ci200274qopenalex-snapshot
DSX: A Knowledge-Based Scoring Function for the Assessment of Protein–Ligand Complexes
inferred← citeshttps://doi.org/10.1021/ci700134popenalex-snapshot
DrugScoreRNAKnowledge-Based Scoring Function To Predict RNA−Ligand Interactions
inferred← citeshttps://doi.org/10.1063/1.3498743openalex-snapshot
Sequence composition and environment effects on residue fluctuations in protein structures
inferred← citeshttps://doi.org/10.1093/bioinformatics/btp108openalex-snapshot
The ruggedness of protein–protein energy landscape and the cutoff for 1/r n potentials
inferred← citeshttps://doi.org/10.1093/bioinformatics/bts182openalex-snapshot
Ligand-binding site prediction using ligand-interacting and binding site-enriched protein triangles
inferred← citeshttps://doi.org/10.1186/1471-2105-11-298openalex-snapshot
An interaction-motif-based scoring function for protein-ligand docking
inferred← citeshttps://doi.org/10.1529/biophysj.108.135814openalex-snapshot
DARS (Decoys As the Reference State) Potentials for Protein-Protein Docking
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