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Automated site preparation in physics‐based rescoring of receptor ligand complexes

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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)1097-0134(199612)26:4<363::aid-prot1>3.0.co;2-dopenalex-snapshot

Positioning hydrogen atoms by optimizing hydrogen-bond networks in protein structures

inferredcites →https://doi.org/10.1002/(sici)1097-0134(20000601)39:4<393::aid-prot120>3.0.co;2-hopenalex-snapshot

Examining methods for calculations of binding free energies: LRA, LIE, PDLD-LRA, and PDLD/S-LRA calculations of ligands binding to an HIV protease

inferredcites →https://doi.org/10.1002/0470020571.ch10openalex-snapshot

The Protein Databank

inferredcites →https://doi.org/10.1002/jcc.20372openalex-snapshot

Linear‐scaling molecular orbital calculations for the pKa values of ionizable residues in proteins

inferredcites →https://doi.org/10.1002/jcc.20505openalex-snapshot

An iterative knowledge‐based scoring function to predict protein–ligand interactions: II. Validation of the scoring function

inferredcites →https://doi.org/10.1002/jcc.20580openalex-snapshot

Role of binding entropy in the refinement of protein–ligand docking predictions: Analysis based on the use of 11 scoring functions

inferredcites →https://doi.org/10.1002/jcc.20821openalex-snapshot

Accurate prediction of protonation state as a prerequisite for reliable MM‐PB(GB)SA binding free energy calculations of HIV‐1 protease inhibitors

inferredcites →https://doi.org/10.1002/jcc.540130714openalex-snapshot

Validation of the general purpose QUANTA ®3.2/CHARMm® force field

inferredcites →https://doi.org/10.1002/prot.10613openalex-snapshot

A hierarchical approach to all‐atom protein loop prediction

inferredcites →https://doi.org/10.1002/prot.20014openalex-snapshot

High‐resolution prediction of protein helix positions and orientations

inferredcites →https://doi.org/10.1002/prot.21065openalex-snapshot

Structure modeling, ligand binding, and binding affinity calculation (LR‐MM‐PBSA) of human heparanase for inhibition and drug design

inferredcites →https://doi.org/10.1002/prot.21082openalex-snapshot

Protein–ligand docking: Current status and future challenges

inferredcites →https://doi.org/10.1002/prot.21125openalex-snapshot

Assignment of polar states for protein amino acid residues using an interaction cluster decomposition algorithm and its application to high resolution protein structure modeling

inferredcites →https://doi.org/10.1002/prot.21382openalex-snapshot

Accuracy of binding mode prediction with a cascadic stochastic tunneling method

inferredcites →https://doi.org/10.1002/prot.21423openalex-snapshot

FLIPDock: Docking flexible ligands into flexible receptors

inferredcites →https://doi.org/10.1002/prot.21603openalex-snapshot

Efficient comprehensive scoring of docked protein complexes using probabilistic support vector machines

inferredcites →https://doi.org/10.1002/prot.21607openalex-snapshot

Receptor‐specific scoring functions derived from quantum chemical models improve affinity estimates for in‐silico drug discovery

inferredcites →https://doi.org/10.1002/prot.21657openalex-snapshot

Protein–protein binding is often associated with changes in protonation state

inferredcites →https://doi.org/10.1002/prot.21782openalex-snapshot

A general approach for developing system‐specific functions to score protein–ligand docked complexes using support vector inductive logic programming

inferredcites →https://doi.org/10.1002/prot.21818openalex-snapshot

Modeling of metal interaction geometries for protein–ligand docking

inferredcites →https://doi.org/10.1002/prot.21844openalex-snapshot

A statistical rescoring scheme for protein–ligand docking: Consideration of entropic effect

inferredcites →https://doi.org/10.1002/prot.21847openalex-snapshot

High quality binding modes in docking ligands to proteins

inferredcites →https://doi.org/10.1002/prot.22102openalex-snapshot

Very fast prediction and rationalization of pKa values for protein–ligand complexes

inferredcites →https://doi.org/10.1006/jmbi.1994.1258openalex-snapshot

Structural Origins of pH and Ionic Strength Effects on Protein Stability

inferredcites →https://doi.org/10.1006/jmbi.1998.2401openalex-snapshot

Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation 1 1Edited by J. Thornton

inferredcites →https://doi.org/10.1007/s10822-007-9133-zopenalex-snapshot

Epik: a software program for pK a prediction and protonation state generation for drug-like molecules

inferredcites →https://doi.org/10.1007/s10822-007-9151-xopenalex-snapshot

Bias, reporting, and sharing: computational evaluations of docking methods

inferredcites →https://doi.org/10.1007/s10822-007-9165-4openalex-snapshot

Can we use docking and scoring for hit-to-lead optimization?

inferredcites →https://doi.org/10.1007/s10822-008-9188-5openalex-snapshot

A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE)

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WHAT IF: A molecular modeling and drug design program

inferredcites →https://doi.org/10.1016/j.bbapap.2007.10.005openalex-snapshot

Flexible ligand–flexible protein docking in protein kinase systems

inferredcites →https://doi.org/10.1016/j.bmc.2007.08.019openalex-snapshot

Validation of an automated procedure for the prediction of relative free energies of binding on a set of aldose reductase inhibitors

inferredcites →https://doi.org/10.1016/j.bmcl.2007.06.095openalex-snapshot

Theoretical calculation of the binding free energies for pyruvate dehydrogenase E1 binding with ligands

inferredcites →https://doi.org/10.1016/j.ejmech.2006.12.037openalex-snapshot

The consequences of scoring docked ligand conformations using free energy correlations

inferredcites →https://doi.org/10.1016/j.jmb.2007.01.022openalex-snapshot

Protonation Changes upon Ligand Binding to Trypsin and Thrombin: Structural Interpretation Based on pKa Calculations and ITC Experiments

inferredcites →https://doi.org/10.1016/j.jmb.2008.01.049openalex-snapshot

Rescoring Docking Hit Lists for Model Cavity Sites: Predictions and Experimental Testing

inferredcites →https://doi.org/10.1016/s0006-3495(02)73940-4openalex-snapshot

Combining Conformational Flexibility and Continuum Electrostatics for Calculating pKas in Proteins

inferredcites →https://doi.org/10.1021/bi00496a010openalex-snapshot

pKa's of ionizable groups in proteins: atomic detail from a continuum electrostatic model

inferredcites →https://doi.org/10.1021/bi00514a028openalex-snapshot

Calculations of enzymic reactions: calculations of pKa, proton transfer reactions, and general acid catalysis reactions in enzymes

inferredcites →https://doi.org/10.1021/bi700822gopenalex-snapshot

Caught in the Act: The 1.5 Å Resolution Crystal Structures of the HIV-1 Protease and the I54V Mutant Reveal a Tetrahedral Reaction Intermediate

inferredcites →https://doi.org/10.1021/ci050283kopenalex-snapshot

Comparison of Consensus Scoring Strategies for Evaluating Computational Models of Protein−Ligand Complexes

inferredcites →https://doi.org/10.1021/ci0502855openalex-snapshot

Physics-Based Scoring of Protein−Ligand Complexes: Enrichment of Known Inhibitors in Large-Scale Virtual Screening

inferredcites →https://doi.org/10.1021/ci050296yopenalex-snapshot

The Use of Consensus Scoring in Ligand-Based Virtual Screening

inferredcites →https://doi.org/10.1021/ci0503255openalex-snapshot

On Evaluating Molecular-Docking Methods for Pose Prediction and Enrichment Factors

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Solvated Interaction Energy (SIE) for Scoring Protein−Ligand Binding Affinities. 1. Exploring the Parameter Space

inferredcites →https://doi.org/10.1021/ci700224eopenalex-snapshot

Distance Dependent Scoring Function for Describing Protein−Ligand Intermolecular Interactions

inferredcites →https://doi.org/10.1021/ci700239topenalex-snapshot

Consensus Scoring with Feature Selection for Structure-Based Virtual Screening

inferredcites →https://doi.org/10.1021/ci7003626openalex-snapshot

Maximum Common Binding Modes (MCBM): Consensus Docking Scoring Using Multiple Ligand Information and Interaction Fingerprints

inferredcites →https://doi.org/10.1021/ct600129fopenalex-snapshot

Multiscale Optimization of a Truncated Newton Minimization Algorithm and Application to Proteins and Protein−Ligand Complexes

inferredcites →https://doi.org/10.1021/ct6003406openalex-snapshot

Improving Docking Accuracy through Molecular Mechanics Generalized Born Optimization and Scoring

inferredcites →https://doi.org/10.1021/ja801269xopenalex-snapshot

The Catalytic Mechanism of an Aspartic Proteinase Explored with Neutron and X-ray Diffraction

inferredcites →https://doi.org/10.1021/ja9621760openalex-snapshot

Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids

inferredcites →https://doi.org/10.1021/jm000467kopenalex-snapshot

Ligand−Protein DataBase: Linking Protein−Ligand Complex Structures to Binding Data

inferredcites →https://doi.org/10.1021/jm030489hopenalex-snapshot

Assessing Scoring Functions for Protein−Ligand Interactions

inferredcites →https://doi.org/10.1021/jm0306430openalex-snapshot

Glide: A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy

inferredcites →https://doi.org/10.1021/jm030644sopenalex-snapshot

Glide: A New Approach for Rapid, Accurate Docking and Scoring. 2. Enrichment Factors in Database Screening

inferredcites →https://doi.org/10.1021/jm0491187openalex-snapshot

Decoys for Docking

inferredcites →https://doi.org/10.1021/jm050040jopenalex-snapshot

Parameter Estimation for Scoring Protein−Ligand Interactions Using Negative Training Data

inferredcites →https://doi.org/10.1021/jm050362nopenalex-snapshot

A Critical Assessment of Docking Programs and Scoring Functions

inferredcites →https://doi.org/10.1021/jm050540copenalex-snapshot

Novel Procedure for Modeling Ligand/Receptor Induced Fit Effects

inferredcites →https://doi.org/10.1021/jm051256oopenalex-snapshot

Extra Precision Glide: Docking and Scoring Incorporating a Model of Hydrophobic Enclosure for Protein−Ligand Complexes

inferredcites →https://doi.org/10.1021/jm060522aopenalex-snapshot

Accurate Prediction of the Relative Potencies of Members of a Series of Kinase Inhibitors Using Molecular Docking and MM-GBSA Scoring

inferredcites →https://doi.org/10.1021/jm060999mopenalex-snapshot

Prediction of Protein−Ligand Interactions. Docking and Scoring: Successes and Gaps

inferredcites →https://doi.org/10.1021/jm070593popenalex-snapshot

A Flexible Approach to Induced Fit Docking

inferredcites →https://doi.org/10.1021/jm070654jopenalex-snapshot

Discovery of Kinase Inhibitors by High-Throughput Docking and Scoring Based on a Transferable Linear Interaction Energy Model

inferredcites →https://doi.org/10.1021/jm7012198openalex-snapshot

Combining Docking, Molecular Dynamics and the Linear Interaction Energy Method to Predict Binding Modes and Affinities for Non-nucleoside Inhibitors to HIV-1 Reverse Transcriptase

inferredcites →https://doi.org/10.1021/jp003919dopenalex-snapshot

Evaluation and Reparametrization of the OPLS-AA Force Field for Proteins via Comparison with Accurate Quantum Chemical Calculations on Peptides

inferredcites →https://doi.org/10.1021/jp021564nopenalex-snapshot

Force Field Validation Using Protein Side Chain Prediction

inferredcites →https://doi.org/10.1021/jp0544639openalex-snapshot

Binding of Phosphinate and Phosphonate Inhibitors to Aspartic Proteases: A First-Principles Study

inferredcites →https://doi.org/10.1021/jp055849mopenalex-snapshot

pKa Prediction Using Group Philicity

inferredcites →https://doi.org/10.1021/jp060334wopenalex-snapshot

Electrostatics of Ligand Binding: Parametrization of the Generalized Born Model and Comparison with the Poisson−Boltzmann Approach

inferredcites →https://doi.org/10.1021/jp963412wopenalex-snapshot

Consistent Calculations of pKa's of Ionizable Residues in Proteins: Semi-microscopic and Microscopic Approaches

inferredcites →https://doi.org/10.1021/jp982533oopenalex-snapshot

Generalized Born Model Based on a Surface Integral Formulation

inferredcites →https://doi.org/10.1038/sj.bjp.0707515openalex-snapshot

Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go

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Molecular mechanics methods for predicting protein–ligand binding

inferredcites →https://doi.org/10.1093/nar/28.1.235openalex-snapshot

The Protein Data Bank

inferredcites →https://doi.org/10.1093/protein/10.12.1363openalex-snapshot

A fast estimate of electrostatic group contributions to the free energy of protein-inhibitor binding

inferredcites →https://doi.org/10.1093/protein/5.3.215openalex-snapshot

Calculations of antibody-antigen interactions: microscopic and semi-microscopic evaluation of the free energies of binding of phosphorylcholine analogs to McPC603

inferredcites →https://doi.org/10.1110/ps.062538707openalex-snapshot

Redesigning protein pKavalues

inferredcites →https://doi.org/10.1110/ps.9.9.1801openalex-snapshot

Thermodynamic dissection of the binding energetics of KNI‐272, a potent HIV‐1 protease inhibitor

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Computational methods in drug discovery

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