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Comparative Evaluation of 11 Scoring Functions for Molecular Docking
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
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The particle concept: placing discrete water molecules during protein-ligand docking predictions
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Effect of ligand volume correction on PMF scoring
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ConsDock: A new program for the consensus analysis of protein–ligand interactions
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A Fast Flexible Docking Method using an Incremental Construction Algorithm
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Development and validation of a genetic algorithm for flexible docking 1 1Edited by F. E. Cohen
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Knowledge-based scoring function to predict protein-ligand interactions
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A knowledge-based scoring function for protein-ligand interactions: Probing the reference state
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The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure
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SCORE: A New Empirical Method for Estimating the Binding Affinity of a Protein-Ligand Complex
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Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: conformationally flexible docking by evolutionary programming
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Protein folding: the free energy surface
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Consensus scoring for ligand/protein interactions
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Reduced Dimensionality in Ligand—Protein Structure Prediction: Covalent Inhibitors of Serine Proteases and Design of Site-Directed Combinatorial Libraries
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How Does Consensus Scoring Work for Virtual Library Screening? An Idealized Computer Experiment
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A new force field for molecular mechanical simulation of nucleic acids and proteins
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Biosynthetic origin of the carbon skeleton and oxygen atoms of nargenicin A1
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Detailed Analysis of Scoring Functions for Virtual Screening
inferredcites →https://doi.org/10.1021/jm001044lopenalex-snapshot
Protein-Based Virtual Screening of Chemical Databases. 1. Evaluation of Different Docking/Scoring Combinations
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A New Concept for Multidimensional Selection of Ligand Conformations (MultiSelect) and Multidimensional Scoring (MultiScore) of Protein−Ligand Binding Affinities
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SMall Molecule Growth 2001 (SMoG2001): An Improved Knowledge-Based Scoring Function for Protein−Ligand Interactions
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A General and Fast Scoring Function for Protein−Ligand Interactions: A Simplified Potential Approach
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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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Prediction of binding constants of protein ligands: A fast method for the prioritization of hits obtained from de novo design or 3D database search programs
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A knowledge-based scoring function for protein-ligand interactions: Probing the reference state
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Further development and validation of empirical scoring functions for structure-based binding affinity prediction
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inferred← citeshttps://doi.org/10.1007/s00706-011-0699-8openalex-snapshot
Synthesis, structure elucidation, DNA interaction, biological evaluation, and molecular docking of an isatin-derived tyramine bidentate Schiff base and its metal complexes
inferred← citeshttps://doi.org/10.1007/s00894-008-0390-0openalex-snapshot
How sophisticated should a scoring function be to ensure successful docking, scoring and virtual screening?
inferred← citeshttps://doi.org/10.1007/s00894-009-0519-9openalex-snapshot
Insight into ligand selectivity in HCV NS5B polymerase: molecular dynamics simulations, free energy decomposition and docking
inferred← citeshttps://doi.org/10.1007/s00894-009-0598-7openalex-snapshot
A fast protein-ligand docking algorithm based on hydrogen bond matching and surface shape complementarity
inferred← citeshttps://doi.org/10.1007/s00894-010-0821-6openalex-snapshot
Structure-based in-silico rational design of a selective peptide inhibitor for thymidine monophosphate kinase of mycobacterium tuberculosis
inferred← citeshttps://doi.org/10.1007/s00894-010-0943-xopenalex-snapshot
Ligand supported homology modeling and docking evaluation of CCR2: docked pose selection by consensus scoring
inferred← citeshttps://doi.org/10.1007/s00894-011-1066-8openalex-snapshot
Computer-aided de novo ligand design and docking/molecular dynamics study of Vitamin D receptor agonists
inferred← citeshttps://doi.org/10.1007/s00894-011-1083-7openalex-snapshot
Molecular dynamics simulation and density functional theory studies on the active pocket for the binding of paclitaxel to tubulin
inferred← citeshttps://doi.org/10.1007/s00894-012-1369-4openalex-snapshot
Molecular docking studies of protein-nucleotide complexes using MOLSDOCK (mutually orthogonal Latin squares DOCK)
inferred← citeshttps://doi.org/10.1007/s00894-012-1416-1openalex-snapshot
FDA approved drugs complexed to their targets: evaluating pose prediction accuracy of docking protocols
inferred← citeshttps://doi.org/10.1007/s00894-012-1479-zopenalex-snapshot
Application of docking-based comparative intermolecular contacts analysis to validate Hsp90α docking studies and subsequent in silico screening for inhibitors
inferred← citeshttps://doi.org/10.1007/s10055-009-0136-zopenalex-snapshot
Multisensory VR interaction for protein-docking in the CoRSAIRe project
inferred← citeshttps://doi.org/10.1007/s10822-004-6258-1openalex-snapshot
Docking studies on NSAID/COX-2 isozyme complexes using Contact Statistics analysis
inferred← citeshttps://doi.org/10.1007/s10822-005-3693-6openalex-snapshot
Multiple ligand-binding modes in bacterial R67 dihydrofolate reductase
inferred← citeshttps://doi.org/10.1007/s10822-006-9041-7openalex-snapshot
Protein Alpha Shape (PAS) Dock: A new gaussian-based score function suitable for docking in homology modelled protein structures
inferred← citeshttps://doi.org/10.1007/s10822-006-9091-xopenalex-snapshot
Ultrafast de novo docking combining pharmacophores and combinatorics
inferred← citeshttps://doi.org/10.1007/s10822-007-9103-5openalex-snapshot
TrixX: structure-based molecule indexing for large-scale virtual screening in sublinear time
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/10.1007/s10822-007-9130-2openalex-snapshot
Molecular modeling on pyruvate phosphate dikinase of Entamoeba histolytica and in silico virtual screening for novel inhibitors
inferred← citeshttps://doi.org/10.1007/s10822-007-9165-4openalex-snapshot
Can we use docking and scoring for hit-to-lead optimization?
inferred← citeshttps://doi.org/10.1007/s10822-008-9199-2openalex-snapshot
Differentiation of AmpC beta-lactamase binders vs. decoys using classification kNN QSAR modeling and application of the QSAR classifier to virtual screening
inferred← citeshttps://doi.org/10.1007/s10822-008-9216-5openalex-snapshot
A new peptide docking strategy using a mean field technique with mutually orthogonal Latin square sampling
inferred← citeshttps://doi.org/10.1007/s10822-008-9224-5openalex-snapshot
Structure-based design of Aurora A & B inhibitors
inferred← citeshttps://doi.org/10.1007/s10822-008-9258-8openalex-snapshot
Scoring confidence index: statistical evaluation of ligand binding mode predictions
inferred← citeshttps://doi.org/10.1007/s10822-009-9296-xopenalex-snapshot
Knowing when to give up: early-rejection stratagems in ligand docking
inferred← citeshttps://doi.org/10.1007/s10822-009-9314-zopenalex-snapshot
A comparative study of AutoDock and PMF scoring performances, and SAR of 2-substituted pyrazolotriazolopyrimidines and 4-substituted pyrazolopyrimidines as potent xanthine oxidase inhibitors
inferred← citeshttps://doi.org/10.1007/s10822-010-9399-4openalex-snapshot
Computer-assisted combinatorial design of bicyclic thymidine analogs as inhibitors of Mycobacterium tuberculosis thymidine monophosphate kinase
inferred← citeshttps://doi.org/10.1007/s10822-012-9564-zopenalex-snapshot
A collaborative environment for developing and validating predictive tools for protein biophysical characteristics
inferred← citeshttps://doi.org/10.1007/s10822-012-9570-1openalex-snapshot
Variability in docking success rates due to dataset preparation
inferred← citeshttps://doi.org/10.1007/s10822-014-9740-4openalex-snapshot
The use of docking-based comparative intermolecular contacts analysis to identify optimal docking conditions within glucokinase and to discover of new GK activators
inferred← citeshttps://doi.org/10.1007/s10822-016-9960-xopenalex-snapshot
A D3R prospective evaluation of machine learning for protein-ligand scoring
inferred← citeshttps://doi.org/10.1007/s10822-017-0030-9openalex-snapshot
GalaxyDock BP2 score: a hybrid scoring function for accurate protein–ligand docking
inferred← citeshttps://doi.org/10.1007/s10822-017-0068-8openalex-snapshot
Convex-PL: a novel knowledge-based potential for protein-ligand interactions deduced from structural databases using convex optimization
inferred← citeshttps://doi.org/10.1007/s10822-017-0072-zopenalex-snapshot
Workflows and performances in the ranking prediction of 2016 D3R Grand Challenge 2: lessons learned from a collaborative effort
inferred← citeshttps://doi.org/10.1007/s10822-017-0081-yopenalex-snapshot
Lessons learned in induced fit docking and metadynamics in the Drug Design Data Resource Grand Challenge 2
inferred← citeshttps://doi.org/10.1007/s10822-018-0146-6openalex-snapshot
Mathematical deep learning for pose and binding affinity prediction and ranking in D3R Grand Challenges
inferred← citeshttps://doi.org/10.1007/s10822-019-00201-3openalex-snapshot
Evaluating the performance of MM/PBSA for binding affinity prediction using class A GPCR crystal structures
inferred← citeshttps://doi.org/10.1007/s10822-019-00211-1openalex-snapshot
Rational creation and systematic analysis of cervical cancer kinase–inhibitor binding profile
inferred← citeshttps://doi.org/10.1007/s10822-020-00318-wopenalex-snapshot
Computational exploration and experimental validation to identify a dual inhibitor of cholinesterase and amyloid-beta for the treatment of Alzheimer’s disease
inferred← citeshttps://doi.org/10.1007/s10895-016-1986-xopenalex-snapshot
Correlation Between Molecular Modelling and Spectroscopic Techniques in Investigation With DNA Binding Interaction of Ruthenium(II) Complexes
inferred← citeshttps://doi.org/10.1007/s11030-006-9037-1openalex-snapshot
Scoring of KDR Kinase Inhibitors: Using Interaction Energy as a Guide for Ranking
inferred← citeshttps://doi.org/10.1007/s11030-009-9172-6openalex-snapshot
In silico structure-based design of a novel class of potent and selective small peptide inhibitor of Mycobacterium tuberculosis Dihydrofolate reductase, a potential target for anti-TB drug discovery
inferred← citeshttps://doi.org/10.1007/s11030-010-9288-8openalex-snapshot
Discriminating of HMG-CoA reductase inhibitors and decoys using self-organizing maps
inferred← citeshttps://doi.org/10.1007/s11030-017-9747-6openalex-snapshot
Identification of potential trypanothione reductase inhibitors among commercially available $$\upbeta $$ β -carboline derivatives using chemical space, lead-like and drug-like filters, pharmacophore models and molecular docking
inferred← citeshttps://doi.org/10.1007/s11030-022-10542-1openalex-snapshot
Synthesis, characterization and evaluation of prenylated chalcones ethers as promising antileishmanial compounds
inferred← citeshttps://doi.org/10.1007/s11094-020-02188-wopenalex-snapshot
Synthesis, Cytotoxic Activity and Molecular Docking Studies of New Condensed Thieno[2,3-d]Pyrimidines as Antitumor Agents
inferred← citeshttps://doi.org/10.1007/s12272-014-0495-1openalex-snapshot
Structure-based lead discovery for protein kinase C zeta inhibitor design by exploiting kinase–inhibitor complex crystal structure data and potential therapeutics for preterm labour
inferred← citeshttps://doi.org/10.1007/s12272-015-0640-5openalex-snapshot
Role of computer-aided drug design in modern drug discovery
inferred← citeshttps://doi.org/10.1007/s12539-011-0071-zopenalex-snapshot
In silico prediction and characterization of 3D structure and binding properties of catalase from the commercially important crab, Scylla serrata
inferred← citeshttps://doi.org/10.1007/s12539-013-0150-4openalex-snapshot
In silico prediction of 3D structure of Mn superoxide dismutase of Scylla serrata and its binding properties with inhibitors
inferred← citeshttps://doi.org/10.1007/s12539-015-0110-2openalex-snapshot
Investigating the Conformational Structure and Potential Site Interactions of SOD Inhibitors on Ec-SOD in Marine Mud Crab Scylla serrata: A Molecular Modeling Approach
inferred← citeshttps://doi.org/10.1007/s12551-013-0130-2openalex-snapshot
Receptor–ligand molecular docking
inferred← citeshttps://doi.org/10.1007/s40199-022-00445-9openalex-snapshot
Alpinumisoflavone against cancer pro-angiogenic targets: In silico, In vitro, and In ovo evaluation
inferred← citeshttps://doi.org/10.1007/s44371-026-00848-6openalex-snapshot
Advanced techniques in molecular docking of inorganic complexes for understanding biological relationships
inferred← citeshttps://doi.org/10.1016/b0-08-045044-x/00241-8openalex-snapshot
Introduction to Computer-Assisted Drug Design – Overview and Perspective for the Future
inferred← citeshttps://doi.org/10.1016/b0-08-045044-x/00270-4openalex-snapshot
Seven Transmembrane G Protein-Coupled Receptors: Insights for Drug Design from Structure and Modeling
inferred← citeshttps://doi.org/10.1016/b978-0-12-409547-2.12352-2openalex-snapshot
Molecular Docking—A Solved Problem?
inferred← citeshttps://doi.org/10.1016/b978-0-12-417205-0.00006-7openalex-snapshot
In Silico Screening
inferred← citeshttps://doi.org/10.1016/b978-0-12-802508-6.00027-2openalex-snapshot
Practical Considerations in Virtual Screening and Molecular Docking
inferred← citeshttps://doi.org/10.1016/b978-0-12-813691-1.00001-4openalex-snapshot
Exploring the binding potential of carbon nanotubes and fullerene towards major drug targets of multidrug resistant bacterial pathogens and their utility as novel therapeutic agents
inferred← citeshttps://doi.org/10.1016/b978-0-12-816125-8.00006-7openalex-snapshot
Molecular Docking: A Structure-Based Approach for Drug Repurposing
inferred← citeshttps://doi.org/10.1016/b978-0-12-819497-3.00015-5openalex-snapshot
In silico development of quorum sensing inhibitors
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