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An Extensive Test of 14 Scoring Functions Using the PDBbind Refined Set of 800 Protein−Ligand Complexes
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Knowledge-based scoring function to predict protein-ligand interactions
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How Does Consensus Scoring Work for Virtual Library Screening? An Idealized Computer Experiment
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Comparison of Ranking Methods for Virtual Screening in Lead-Discovery Programs
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Molecular Recognition of Protein−Ligand Complexes: Applications to Drug Design
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An Extended Linear Response Method for Determining Free Energies of Hydration
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Detailed Analysis of Scoring Functions for Virtual Screening
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Ligand−Protein DataBase: Linking Protein−Ligand Complex Structures to Binding Data
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Protein-Based Virtual Screening of Chemical Databases. 1. Evaluation of Different Docking/Scoring Combinations
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Evaluation of Docking Functions for Protein−Ligand Docking
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SMall Molecule Growth 2001 (SMoG2001): An Improved Knowledge-Based Scoring Function for Protein−Ligand Interactions
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Simple, Intuitive Calculations of Free Energy of Binding for Protein−Ligand Complexes. 1. Models without Explicit Constrained Water
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Assessing Scoring Functions for Protein−Ligand Interactions
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Glide: A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy
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Consensus Scoring: A Method for Obtaining Improved Hit Rates from Docking Databases of Three-Dimensional Structures into Proteins
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Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes
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Empirical scoring functions. II. The testing of an empirical scoring function for the prediction of ligand-receptor binding affinities and the use of Bayesian regression to improve the quality of the model
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Deciphering common failures in molecular docking of ligand-protein complexes
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A knowledge-based scoring function for protein-ligand interactions: Probing the reference state
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Combined molecular mechanical and continuum solvent approach (MM-PBSA/GBSA) to predict ligand binding
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Predicting binding modes, binding affinities and `hot spots' for protein-ligand complexes using a knowledge-based scoring function
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Further development and validation of empirical scoring functions for structure-based binding affinity prediction
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Protein Ligand Database (PLD): additional understanding of the nature and specificity of protein–ligand complexes
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A new method for predicting binding affinity in computer-aided drug design
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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
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Incoming claims: where this work appears in other papers’ reference lists and arguments.
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Ligand Identification Scoring Algorithm (LISA)
inferred← citeshttps://doi.org/10.1021/ci300034xopenalex-snapshot
PROLIX: Rapid Mining of Protein–Ligand Interactions in Large Crystal Structure Databases
inferred← citeshttps://doi.org/10.1021/ci3002638openalex-snapshot
Integrating Ligand-Based and Protein-Centric Virtual Screening of Kinase Inhibitors Using Ensembles of Multiple Protein Kinase Genes and Conformations
inferred← citeshttps://doi.org/10.1021/ci300417yopenalex-snapshot
How to Improve Docking Accuracy of AutoDock4.2: A Case Study Using Different Electrostatic Potentials
inferred← citeshttps://doi.org/10.1021/ci400037yopenalex-snapshot
Highly SpecIfic and Sensitive Pharmacophore Model for Identifying CXCR4 Antagonists. Comparison with Docking and Shape-Matching Virtual Screening Performance
inferred← citeshttps://doi.org/10.1021/ci400067copenalex-snapshot
Improving the Scoring of Protein–Ligand Binding Affinity by Including the Effects of Structural Water and Electronic Polarization
inferred← citeshttps://doi.org/10.1021/ci400321ropenalex-snapshot
Computation of Binding Energies Including Their Enthalpy and Entropy Components for Protein–Ligand Complexes Using Support Vector Machines
inferred← citeshttps://doi.org/10.1021/ci400427aopenalex-snapshot
Assessing Molecular Docking Tools for Relative Biological Activity Prediction: A Case Study of Triazole HIV-1 NNRTIs
inferred← citeshttps://doi.org/10.1021/ci600267kopenalex-snapshot
Synergistic Use of Compound Properties and Docking Scores in Neural Network Modeling of CYP2D6 Binding: Predicting Affinity and Conformational Sampling
inferred← citeshttps://doi.org/10.1021/ci600406vopenalex-snapshot
Solvated Interaction Energy (SIE) for Scoring Protein−Ligand Binding Affinities. 1. Exploring the Parameter Space
inferred← citeshttps://doi.org/10.1021/ci600412zopenalex-snapshot
Comparative Evaluation of MMPBSA and XSCORE To Compute Binding Free Energy in XIAP−Peptide Complexes
inferred← citeshttps://doi.org/10.1021/ci7001236openalex-snapshot
GlamDock: Development and Validation of a New Docking Tool on Several Thousand Protein−Ligand Complexes
inferred← citeshttps://doi.org/10.1021/ci7002472openalex-snapshot
Consensus Adaptation of Fields for Molecular Comparison (AFMoC) Models Incorporate Ligand and Receptor Conformational Variability into Tailor-made Scoring Functions
inferred← citeshttps://doi.org/10.1021/ci8001167openalex-snapshot
MedusaScore: An Accurate Force Field-Based Scoring Function for Virtual Drug Screening
inferred← citeshttps://doi.org/10.1021/ci800125kopenalex-snapshot
Information Theory-Based Scoring Function for the Structure-Based Prediction of Protein−Ligand Binding Affinity
inferred← citeshttps://doi.org/10.1021/ci800149wopenalex-snapshot
Computationally Identified Novel Diphenyl- and Phenylpyridine Androgen Receptor Antagonist Structures
inferred← citeshttps://doi.org/10.1021/ci8004308openalex-snapshot
Docking Ligands into Flexible and Solvated Macromolecules. 4. Are Popular Scoring Functions Accurate for this Class of Proteins?
inferred← citeshttps://doi.org/10.1021/ci8004429openalex-snapshot
Interpretation of the Binding Affinities of PTP1B Inhibitors with the MM-GB/SA Method and the X-Score Scoring Function
inferred← citeshttps://doi.org/10.1021/ci9000053openalex-snapshot
Comparative Assessment of Scoring Functions on a Diverse Test Set
inferred← citeshttps://doi.org/10.1021/ci9004139openalex-snapshot
Binding Affinity Prediction with Property-Encoded Shape Distribution Signatures
inferred← citeshttps://doi.org/10.1021/ja064863popenalex-snapshot
Relationship Among Ligand Conformations in Solution, in the Solid State, and at the Hsp90 Binding Site: Geldanamycin and Radicicol
inferred← citeshttps://doi.org/10.1021/jm048957qopenalex-snapshot
The PDBbind Database: Methodologies and Updates
inferred← citeshttps://doi.org/10.1021/jm050043wopenalex-snapshot
M-Score: A Knowledge-Based Potential Scoring Function Accounting for Protein Atom Mobility
inferred← citeshttps://doi.org/10.1021/jm050114ropenalex-snapshot
Improving Binding Mode Predictions by Docking into Protein-Specifically Adapted Potential Fields
inferred← citeshttps://doi.org/10.1021/jm050362nopenalex-snapshot
A Critical Assessment of Docking Programs and Scoring Functions
inferred← citeshttps://doi.org/10.1021/jm0503751openalex-snapshot
Computational Study of Antagonist/α1AAdrenoceptor ComplexesObservations of Conformational Variations on the Formation of Ligand/Receptor Complexes
inferred← citeshttps://doi.org/10.1021/jm050436vopenalex-snapshot
DrugScore CSD Knowledge-Based Scoring Function Derived from Small Molecule Crystal Data with Superior Recognition Rate of Near-Native Ligand Poses and Better Affinity Prediction
inferred← citeshttps://doi.org/10.1021/jm0508538openalex-snapshot
Catalytic Site Prediction and Virtual Screening of Cytochrome P450 2D6 Substrates by Consideration of Water and Rescoring in Automated Docking
inferred← citeshttps://doi.org/10.1021/jm060023+openalex-snapshot
Discovery of a Nanomolar Inhibitor of the Human Murine Double Minute 2 (MDM2)−p53 Interaction through an Integrated, Virtual Database Screening Strategy
inferred← citeshttps://doi.org/10.1021/jm0608356openalex-snapshot
Benchmarking Sets for Molecular Docking
inferred← citeshttps://doi.org/10.1021/jm9006966openalex-snapshot
Automated Docking Screens: A Feasibility Study
inferred← citeshttps://doi.org/10.1021/tx050301sopenalex-snapshot
Computational Screening of Phthalate Monoesters for Binding to PPARγ
inferred← citeshttps://doi.org/10.1038/nprot.2017.114openalex-snapshot
Assessing protein–ligand interaction scoring functions with the CASF-2013 benchmark
inferred← citeshttps://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
inferred← citeshttps://doi.org/10.1039/9781849735377-00195openalex-snapshot
Binding Free Energy Calculation and Scoring in Small-Molecule Docking
inferred← citeshttps://doi.org/10.1039/c1sc00628bopenalex-snapshot
Arylsulfonamides as inhibitors for carbonic anhydrase: prediction & validation
inferred← citeshttps://doi.org/10.1039/c3mb70503jopenalex-snapshot
Exploring a structural protein–drug interactome for new therapeutics in lung cancer
inferred← citeshttps://doi.org/10.1039/c6ce01056copenalex-snapshot
Designed synthesis of “L” shaped 17-halo-aryl-ethynyl steroids
inferred← citeshttps://doi.org/10.1039/c8cp06555aopenalex-snapshot
The shielding effect of metal complexes on the binding affinities of ligands to metalloproteins
inferred← citeshttps://doi.org/10.1073/pnas.0610202104openalex-snapshot
Motifs for molecular recognition exploiting hydrophobic enclosure in protein–ligand binding
inferred← citeshttps://doi.org/10.1073/pnas.0813396106openalex-snapshot
Calix[4]arene-based conical-shaped ligands for voltage-dependent potassium channels
inferred← citeshttps://doi.org/10.1093/abt/tbab011openalex-snapshot
Application of an integrated computational antibody engineering platform to design SARS-CoV-2 neutralizers
inferred← citeshttps://doi.org/10.1093/bioinformatics/btq112openalex-snapshot
A machine learning approach to predicting protein–ligand binding affinity with applications to molecular docking
inferred← citeshttps://doi.org/10.1099/jgv.0.000500openalex-snapshot
A molecular modelling approach to understand the effect of co-evolutionary mutations (V344M, I354L) identified in the PB2 subunit of influenza A 2009 pandemic H1N1 virus on m7GTP ligand binding
inferred← citeshttps://doi.org/10.1105/tpc.109.072652openalex-snapshot
Crystal Structures of a Populus tomentosa 4-Coumarate:CoA Ligase Shed Light on Its Enzymatic Mechanisms
inferred← citeshttps://doi.org/10.1109/bibm.2009.24openalex-snapshot
GemAffinity: A Scoring Function for Predicting Binding Affinity and Virtual Screening
inferred← citeshttps://doi.org/10.1109/icbbe.2008.46openalex-snapshot
Binding Affinity Analysis of Protein-Ligand Complexes
inferred← citeshttps://doi.org/10.1109/ijcnn.2013.6706909openalex-snapshot
Improving drug discovery using a neural networks based parallel scoring function
inferred← citeshttps://doi.org/10.1109/ipdpsw.2014.65openalex-snapshot
Exploring Large Scale Receptor-Ligand Pairs in Molecular Docking Workflows in HPC Clouds
inferred← citeshttps://doi.org/10.1109/tcbb.2012.36openalex-snapshot
A Comparative Assessment of Ranking Accuracies of Conventional and Machine-Learning-Based Scoring Functions for Protein-Ligand Binding Affinity Prediction
inferred← citeshttps://doi.org/10.1109/tcbb.2014.2351824openalex-snapshot
A Comparative Assessment of Predictive Accuracies of Conventional and Machine Learning Scoring Functions for Protein-Ligand Binding Affinity Prediction
inferred← citeshttps://doi.org/10.1111/j.1747-0285.2011.01157.xopenalex-snapshot
Drug‐like Leads for Steric Discrimination between Substrate and Inhibitors of Human Acetylcholinesterase
inferred← citeshttps://doi.org/10.1111/j.1747-0285.2012.01362.xopenalex-snapshot
Inhibition of Bacterial Virulence: Drug‐Like Molecules Targeting the Salmonella enterica PhoP Response Regulator
inferred← citeshttps://doi.org/10.1134/s0022476615050066openalex-snapshot
QSAR studies of HEPT derivatives as anti-HIV drugs using the RASMS method
inferred← citeshttps://doi.org/10.1134/s1068162010040023openalex-snapshot
Molecular docking: The role of noncovalent interactions in the formation of protein-nucleotide and protein-peptide complexes
inferred← citeshttps://doi.org/10.1142/s0219633608004155openalex-snapshot
POSE SCALING: GEOMETRICAL ASSESSMENT OF LIGAND BINDING POSES
inferred← citeshttps://doi.org/10.1146/annurev.biophys.36.040306.132550openalex-snapshot
Calculation of Protein-Ligand Binding Affinities
inferred← citeshttps://doi.org/10.1155/2014/162150openalex-snapshot
Evaluation of 11 Scoring Functions Performance on Matrix Metalloproteinases
inferred← citeshttps://doi.org/10.1155/2018/3829307openalex-snapshot
Correlation between Virtual Screening Performance and Binding Site Descriptors of Protein Targets
inferred← citeshttps://doi.org/10.11606/t.46.2016.tde-10082016-115529openalex-snapshot
Modelos de virtual Screening de inibidores da cruzaína: desenvolvimento e validação experimental
inferred← citeshttps://doi.org/10.1177/1094342017697471openalex-snapshot
METADOCK: A parallel metaheuristic schema for virtual screening methods
inferred← citeshttps://doi.org/10.1186/1471-2105-11-193openalex-snapshot
A knowledge-guided strategy for improving the accuracy of scoring functions in binding affinity prediction
inferred← citeshttps://doi.org/10.1186/1471-2105-13-s14-s13openalex-snapshot
High-Throughput parallel blind Virtual Screening using BINDSURF
inferred← citeshttps://doi.org/10.1186/1471-2105-16-s4-s8openalex-snapshot
BgN-Score and BsN-Score: Bagging and boosting based ensemble neural networks scoring functions for accurate binding affinity prediction of protein-ligand complexes
inferred← citeshttps://doi.org/10.1186/s12952-016-0058-8openalex-snapshot
Evaluation of a novel virtual screening strategy using receptor decoy binding sites
inferred← citeshttps://doi.org/10.1186/s13015-015-0034-8openalex-snapshot
MoDock: A multi-objective strategy improves the accuracy for molecular docking
inferred← citeshttps://doi.org/10.1186/s13321-015-0095-1openalex-snapshot
BCL::Conf: small molecule conformational sampling using a knowledge based rotamer library
inferred← citeshttps://doi.org/10.1208/s12248-012-9322-0openalex-snapshot
Structure-Based Virtual Screening for Drug Discovery: a Problem-Centric Review
inferred← citeshttps://doi.org/10.12691/ajmo-4-3-2openalex-snapshot
Docking and Ligand Binding Affinity: Uses and Pitfalls
inferred← citeshttps://doi.org/10.1504/ijcbdd.2011.044404openalex-snapshot
Discovering a potent small molecule inhibitor for gankyrin using de novo drug design approach
inferred← citeshttps://doi.org/10.1504/ijdmb.2012.045535openalex-snapshot
GemAffinity: a scoring function for predicting binding affinity and Virtual Screening
inferred← citeshttps://doi.org/10.2174/138161212799436386openalex-snapshot
From Laptop to Benchtop to Bedside: Structure-based Drug Design on Protein Targets
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