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Nonlinear Scoring Functions for Similarity-Based Ligand Docking and Binding Affinity Prediction

https://doi.org/10.1021/ci400510e
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Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/(sici)1096-987x(19981115)19:14<1639::aid-jcc10>3.0.co;2-bopenalex-snapshot
Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
inferredcites →https://doi.org/10.1002/(sici)1099-1352(199601)9:1<1::aid-jmr241>3.0.co;2-6openalex-snapshot
Automated docking of flexible ligands: Applications of autodock
inferredcites →https://doi.org/10.1002/(sici)1099-1352(199603)9:2<175::aid-jmr260>3.0.co;2-dopenalex-snapshot
Molecular docking towards drug discovery
inferredcites →https://doi.org/10.1002/jcc.20022openalex-snapshot
Ligand–protein docking using a quantum stochastic tunneling optimization method
inferredcites →https://doi.org/10.1002/jcc.20175openalex-snapshot
A scoring function for docking ligands to low‐resolution protein structures
inferredcites →https://doi.org/10.1002/jcc.20917openalex-snapshot
Q‐Dock: Low‐resolution flexible ligand docking with pocket‐specific threading restraints
inferredcites →https://doi.org/10.1002/jcc.21256openalex-snapshot
AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility
inferredcites →https://doi.org/10.1002/jcc.21334openalex-snapshot
AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
inferredcites →https://doi.org/10.1002/jcc.21601openalex-snapshot
Predicting the accuracy of protein–ligand docking on homology models
inferredcites →https://doi.org/10.1002/jcc.540150503openalex-snapshot
ICM—A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation
inferredcites →https://doi.org/10.1002/pro.5560070411openalex-snapshot
Flexible ligand docking using conformational ensembles
inferredcites →https://doi.org/10.1002/pro.5560070620openalex-snapshot
Fold prediction by a hierarchy of sequence, threading, and modeling methods
inferredcites →https://doi.org/10.1002/prot.10232openalex-snapshot
A new test set for validating predictions of protein–ligand interaction
inferredcites →https://doi.org/10.1002/prot.10237openalex-snapshot
Protein‐based virtual screening of chemical databases. II. Are homology models of g‐protein coupled receptors suitable targets?
inferredcites →https://doi.org/10.1002/prot.10465openalex-snapshot
Improved protein–ligand docking using GOLD
inferredcites →https://doi.org/10.1002/prot.20264openalex-snapshot
Scoring function for automated assessment of protein structure template quality
inferredcites →https://doi.org/10.1002/prot.340230306openalex-snapshot
Evaluation of comparative protein modeling by M ODELLER
inferredcites →https://doi.org/10.1006/jmbi.1996.0897openalex-snapshot
Development and validation of a genetic algorithm for flexible docking 1 1Edited by F. E. Cohen
inferredcites →https://doi.org/10.1007/s10822-012-9565-yopenalex-snapshot
Evaluation of DOCK 6 as a pose generation and database enrichment tool
inferredcites →https://doi.org/10.1007/s10822-013-9663-5openalex-snapshot
eFindSite: Improved prediction of ligand binding sites in protein models using meta-threading, machine learning and auxiliary ligands
inferredcites →https://doi.org/10.1016/j.bmc.2009.10.024openalex-snapshot
Design, synthesis, and SAR of cis-1,2-diaminocyclohexane derivatives as potent factor Xa inhibitors. Part II: Exploration of 6–6 fused rings as alternative S1 moieties
inferredcites →https://doi.org/10.1016/j.drudis.2006.10.005openalex-snapshot
Similarity-based virtual screening using 2D fingerprints
inferredcites →https://doi.org/10.1016/j.drudis.2011.02.011openalex-snapshot
State-of-the-art in ligand-based virtual screening
inferredcites →https://doi.org/10.1016/j.jmb.2008.11.010openalex-snapshot
RosettaLigand Docking with Full Ligand and Receptor Flexibility
inferredcites →https://doi.org/10.1021/ci000150topenalex-snapshot
Comparison of the NCI Open Database with Seven Large Chemical Structural Databases
inferredcites →https://doi.org/10.1021/ci010132ropenalex-snapshot
Reoptimization of MDL Keys for Use in Drug Discovery
inferredcites →https://doi.org/10.1021/ci030287uopenalex-snapshot
Profile Scaling Increases the Similarity Search Performance of Molecular Fingerprints Containing Numerical Descriptors and Structural Keys
inferredcites →https://doi.org/10.1021/ci034289qopenalex-snapshot
Virtual Screening Using Protein−Ligand Docking: Avoiding Artificial Enrichment
inferredcites →https://doi.org/10.1021/ci049714+openalex-snapshot
ZINC − A Free Database of Commercially Available Compounds for Virtual Screening
inferredcites →https://doi.org/10.1021/ci050238copenalex-snapshot
Screening Drug-Like Compounds by Docking to Homology Models: A Systematic Study
inferredcites →https://doi.org/10.1021/ci100369fopenalex-snapshot
A Machine Learning-Based Method To Improve Docking Scoring Functions and Its Application to Drug Repurposing
inferredcites →https://doi.org/10.1021/ci2001023openalex-snapshot
Build-Up Algorithm for Atomic Correspondence between Chemical Structures
inferredcites →https://doi.org/10.1021/ci200274qopenalex-snapshot
DSX: A Knowledge-Based Scoring Function for the Assessment of Protein–Ligand Complexes
inferredcites →https://doi.org/10.1021/ci600426eopenalex-snapshot
Evaluating Virtual Screening Methods: Good and Bad Metrics for the “Early Recognition” Problem
inferredcites →https://doi.org/10.1021/ci6005646openalex-snapshot
Generating Conformer Ensembles Using a Multiobjective Genetic Algorithm
inferredcites →https://doi.org/10.1021/ci900014fopenalex-snapshot
LQTA-QSAR: A New 4D-QSAR Methodology
inferredcites →https://doi.org/10.1021/ci9002415openalex-snapshot
Conformational Sampling for Large-Scale Virtual Screening: Accuracy versus Ensemble Size
inferredcites →https://doi.org/10.1021/ci900419kopenalex-snapshot
Current Trends in Ligand-Based Virtual Screening: Molecular Representations, Data Mining Methods, New Application Areas, and Performance Evaluation
inferredcites →https://doi.org/10.1021/jm00334a001openalex-snapshot
A Mathematical Contribution to Structure-Activity Studies
inferredcites →https://doi.org/10.1021/jm011005popenalex-snapshot
5D-QSAR: The Key for Simulating Induced Fit?
inferredcites →https://doi.org/10.1021/jm0203783openalex-snapshot
Comparative Evaluation of 11 Scoring Functions for Molecular Docking
inferredcites →https://doi.org/10.1021/jm0300330openalex-snapshot
Information Decay in Molecular Docking Screens against Holo, Apo, and Modeled Conformations of Enzymes
inferredcites →https://doi.org/10.1021/jm0300781openalex-snapshot
Performance of 3D-Database Molecular Docking Studies into Homology Models
inferredcites →https://doi.org/10.1021/jm030209yopenalex-snapshot
Lessons in Molecular Recognition: The Effects of Ligand and Protein Flexibility on Molecular Docking Accuracy
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/jm049113+openalex-snapshot
Anchor−GRIND: Filling the Gap between Standard 3D QSAR and the GRid-INdependent Descriptors
inferredcites →https://doi.org/10.1021/jm049314dopenalex-snapshot
A Knowledge-Based Energy Function for Protein−Ligand, Protein−Protein, and Protein−DNA Complexes
inferredcites →https://doi.org/10.1021/jm050185qopenalex-snapshot
Combining Protein Modeling and 6D-QSAR. Simulating the Binding of Structurally Diverse Ligands to the Estrogen Receptor
inferredcites →https://doi.org/10.1021/jm050540copenalex-snapshot
Novel Procedure for Modeling Ligand/Receptor Induced Fit Effects
inferredcites →https://doi.org/10.1021/jm060186yopenalex-snapshot
Lead Optimization Providing a Series of Flavone Derivatives as Potent Nonsteroidal Inhibitors of the Cytochrome P450 Aromatase Enzyme
inferredcites →https://doi.org/10.1021/jm0608356openalex-snapshot
Benchmarking Sets for Molecular Docking
inferredcites →https://doi.org/10.1021/jm300687eopenalex-snapshot
Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking
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/10.1023/a:1007999920146openalex-snapshot
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
inferredcites →https://doi.org/10.1023/a:1011115820450openalex-snapshot
DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases
inferredcites →https://doi.org/10.1073/pnas.0707684105openalex-snapshot
A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation
inferredcites →https://doi.org/10.1073/pnas.1104614108openalex-snapshot
Pathway and mechanism of drug binding to G-protein-coupled receptors
inferredcites →https://doi.org/10.1074/jbc.274.13.8746openalex-snapshot
Effects of Phosphorylation of Threonine 160 on Cyclin-dependent Kinase 2 Structure and Activity
inferredcites →https://doi.org/10.1093/bioinformatics/15.4.327openalex-snapshot
Automated analysis of interatomic contacts in proteins.
inferredcites →https://doi.org/10.1093/nar/28.1.235openalex-snapshot
The Protein Data Bank
inferredcites →https://doi.org/10.1093/nar/gkg520openalex-snapshot
SWISS-MODEL: an automated protein homology-modeling server
inferredcites →https://doi.org/10.1093/nar/gkl999openalex-snapshot
BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities
inferredcites →https://doi.org/10.1093/nar/gkq325openalex-snapshot
Frog2: Efficient 3D conformation ensemble generator for small compounds
inferredcites →https://doi.org/10.1104/pp.103.024885openalex-snapshot
wCLUTO: A Web-Enabled Clustering Toolkit
inferredcites →https://doi.org/10.1107/s0567739476001873openalex-snapshot
A solution for the best rotation to relate two sets of vectors
inferredcites →https://doi.org/10.1145/1961189.1961199openalex-snapshot
LIBSVM
inferredcites →https://doi.org/10.1186/1471-2105-9-438openalex-snapshot
AMMOS: Automated Molecular Mechanics Optimization tool for in silico Screening
inferredcites →https://doi.org/10.1186/1471-2105-9-531openalex-snapshot
Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score
inferredcites →https://doi.org/10.1186/1758-2946-3-33openalex-snapshot
Open Babel: An open chemical toolbox
inferredcites →https://doi.org/10.1186/1758-2946-5-2openalex-snapshot
Enhanced ranking of PknB Inhibitors using data fusion methods
inferredcites →https://doi.org/10.1371/journal.pcbi.1000405openalex-snapshot
FINDSITELHM: A Threading-Based Approach to Ligand Homology Modeling
inferredcites →https://doi.org/10.1371/journal.pone.0050200openalex-snapshot
eThread: A Highly Optimized Machine Learning-Based Approach to Meta-Threading and the Modeling of Protein Tertiary Structures
inferredcites →https://doi.org/10.2174/1386207003331454openalex-snapshot
Molecular Descriptors in Chemoinformatics, Computational Combinatorial Chemistry, and Virtual Screening
inferredcites →https://doi.org/10.2174/138620709788167962openalex-snapshot
Performance of Machine Learning Methods for Ligand-Based Virtual Screening
inferredcites →https://doi.org/10.2174/138920307781369427openalex-snapshot
Virtual Screening in Drug Discovery - A Computational Perspective
inferredcites →https://doi.org/10.2174/156802610790232260openalex-snapshot
3D-QSAR in Drug Design - A Review
inferredcites →https://doi.org/10.2174/156802610791111489openalex-snapshot
Molecular Shape Technologies in Drug Discovery: Methods and Applications
inferredcites →https://doi.org/10.5860/choice.44-4214openalex-snapshot
Encyclopedia of measurement and statistics

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inferred← citeshttps://doi.org/10.1002/9781119681397.ch23openalex-snapshot
In SilicoPlatforms for Predictive Ecotoxicology
inferred← citeshttps://doi.org/10.1002/jcc.24031openalex-snapshot
GeauxDock: A novel approach for mixed‐resolution ligand docking using a descriptor‐based force field
inferred← citeshttps://doi.org/10.1002/jmr.2471openalex-snapshot
Improvements, trends, and new ideas in molecular docking: 2012–2013 in review
inferred← citeshttps://doi.org/10.1002/prot.24928openalex-snapshot
Different combinations of atomic interactions predict protein‐small molecule and protein‐ DNA/RNA affinities with similar accuracy
inferred← citeshttps://doi.org/10.1007/978-1-0716-4949-7_6openalex-snapshot
Decision Tree for Prediction of Binding Affinity
inferred← citeshttps://doi.org/10.1007/978-1-4939-8736-8_8openalex-snapshot
High-Throughput Reconstruction of Ancestral Protein Sequence, Structure, and Molecular Function
inferred← citeshttps://doi.org/10.1007/s10822-019-00197-wopenalex-snapshot
Elucidating the druggability of the human proteome with eFindSite
inferred← citeshttps://doi.org/10.1007/s10822-021-00423-4openalex-snapshot
Using diverse potentials and scoring functions for the development of improved machine-learned models for protein–ligand affinity and docking pose prediction
inferred← citeshttps://doi.org/10.1007/s12539-019-00327-wopenalex-snapshot
An Overview of Scoring Functions Used for Protein–Ligand Interactions in Molecular Docking
inferred← citeshttps://doi.org/10.1016/b978-0-12-821748-1.00009-9openalex-snapshot
Advances in structure-based drug design
inferred← citeshttps://doi.org/10.1016/b978-0-12-822312-3.00011-4openalex-snapshot
Modern Tools and Techniques in Computer-Aided Drug Design
inferred← citeshttps://doi.org/10.1016/b978-0-323-89925-3.00002-2openalex-snapshot
General considerations on artificial intelligence
inferred← citeshttps://doi.org/10.1016/bs.armc.2022.08.008openalex-snapshot
Can docking scoring functions guarantee success in virtual screening?
inferred← citeshttps://doi.org/10.1016/j.abb.2015.08.002openalex-snapshot
Open challenges in structure-based virtual screening: Receptor modeling, target flexibility consideration and active site water molecules description
inferred← citeshttps://doi.org/10.1016/j.bmcl.2017.11.033openalex-snapshot
Discovery of molecular mechanism of a clinical herbal formula upregulating serum HDL-c levels in treatment of metabolic syndrome by in vivo and computational studies
inferred← citeshttps://doi.org/10.1016/j.ijantimicag.2024.107395openalex-snapshot
Evaluating the antibacterial activity of engineered phage ФEcSw endolysin against multidrug-resistant Escherichia coli strain Sw1
inferred← citeshttps://doi.org/10.1016/j.jmgm.2026.109282openalex-snapshot
RLBindDeep: A ResNet-LSTM based novel framework for protein–ligand binding affinity prediction
inferred← citeshttps://doi.org/10.1021/acs.chemrev.8b00728openalex-snapshot
Concepts of Artificial Intelligence for Computer-Assisted Drug Discovery
inferred← citeshttps://doi.org/10.1021/acs.jcim.5b00036openalex-snapshot
Efficient Heuristics for Maximum Common Substructure Search
inferred← citeshttps://doi.org/10.1021/acs.jcim.7b00049openalex-snapshot
Structural and Sequence Similarity Makes a Significant Impact on Machine-Learning-Based Scoring Functions for Protein–Ligand Interactions
inferred← citeshttps://doi.org/10.1021/acs.jcim.7b00277openalex-snapshot
ProSelection: A Novel Algorithm to Select Proper Protein Structure Subsets for in Silico Target Identification and Drug Discovery Research
inferred← citeshttps://doi.org/10.1021/acsami.0c06207openalex-snapshot
Biomimetic Membrane-Structured Nanovesicles Carrying a Supramolecular Enzyme to Cure Lung Cancer
inferred← citeshttps://doi.org/10.1021/ci500006dopenalex-snapshot
3D Flexible Alignment Using 2D Maximum Common Substructure: Dependence of Prediction Accuracy on Target-Reference Chemical Similarity
inferred← citeshttps://doi.org/10.1073/pnas.2000585117openalex-snapshot
Machine learning classification can reduce false positives in structure-based virtual screening
inferred← citeshttps://doi.org/10.1080/07391102.2021.1905559openalex-snapshot
Application of deep learning and molecular modeling to identify small drug-like compounds as potential HIV-1 entry inhibitors
inferred← citeshttps://doi.org/10.1093/bib/bby061openalex-snapshot
Recent applications of deep learning and machine intelligence on in silico drug discovery: methods, tools and databases
inferred← citeshttps://doi.org/10.1093/bioinformatics/bty816openalex-snapshot
Large-scale prediction of binding affinity in protein–small ligand complexes: the PRODIGY-LIG web server
inferred← citeshttps://doi.org/10.1093/gigascience/giy091openalex-snapshot
eModel-BDB: a database of comparative structure models of drug-target interactions from the Binding Database
inferred← citeshttps://doi.org/10.1093/nar/gkw390openalex-snapshot
CSM-lig: a web server for assessing and comparing protein–small molecule affinities
inferred← citeshttps://doi.org/10.1109/iementech65115.2025.10959578openalex-snapshot
CGDeepAff: Deep Learning-Based Approach for Protein-Ligand Binding Affinity Estimation Using CNN-GRU
inferred← citeshttps://doi.org/10.1109/tnb.2015.2403776openalex-snapshot
Accelerating the Pace of Protein Functional Annotation With Intel Xeon Phi Coprocessors
inferred← citeshttps://doi.org/10.1140/epjqt/s40507-025-00419-1openalex-snapshot
Hybrid quantum neural networks for efficient protein-ligand binding affinity prediction
inferred← citeshttps://doi.org/10.1186/s12859-017-1533-zopenalex-snapshot
Improving the accuracy of high-throughput protein-protein affinity prediction may require better training data
inferred← citeshttps://doi.org/10.1186/s12859-017-1675-zopenalex-snapshot
Across-proteome modeling of dimer structures for the bottom-up assembly of protein-protein interaction networks
inferred← citeshttps://doi.org/10.1186/s13321-016-0126-6openalex-snapshot
A graph-based approach to construct target-focused libraries for virtual screening
inferred← citeshttps://doi.org/10.1371/journal.pone.0296676openalex-snapshot
Improving structure-based protein-ligand affinity prediction by graph representation learning and ensemble learning
inferred← citeshttps://doi.org/10.1515/bams-2014-0024openalex-snapshot
Is the growth rate of Protein Data Bank sufficient to solve the protein structure prediction problem using template-based modeling?
inferred← citeshttps://doi.org/10.15476/elte.2019.029openalex-snapshot
Efficient Algorithms for Graph Optimization Problems
inferred← citeshttps://doi.org/10.21203/rs.3.rs-2192264/v1openalex-snapshot
The efficacy of bacteriophage-encoded endolysin relies on active residues: A molecular perspective
inferred← citeshttps://doi.org/10.2174/1389450117666160112112854openalex-snapshot
Structure-Based Drug Discovery Accelerated by Many-Core Devices
inferred← citeshttps://doi.org/10.2174/1389450122666211214113205openalex-snapshot
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inferred← citeshttps://doi.org/10.3390/biom9100603openalex-snapshot
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inferred← citeshttps://doi.org/10.3390/ijms17091508openalex-snapshot
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inferred← citeshttps://doi.org/10.3390/molecules19044021openalex-snapshot
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inferred← citeshttps://doi.org/10.4018/978-1-5225-0115-2.ch001openalex-snapshot
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inferred← citeshttps://doi.org/10.4018/978-1-5225-0549-5.ch030openalex-snapshot
Molecular Docking at a Glance
inferred← citeshttps://doi.org/10.4155/fdd-2020-0028openalex-snapshot
Artificial Intelligence in Drug Design: Algorithms, Applications, Challenges and Ethics
inferred← citeshttps://doi.org/10.4155/fmc-2018-0525openalex-snapshot
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inferred← citeshttps://doi.org/10.4155/fmc-2021-0243openalex-snapshot
Machine Learning and Deep Learning in Data-Driven Decision Making of Drug Discovery and Challenges in High-Quality Data Acquisition in the Pharmaceutical Industry
inferred← citeshttps://doi.org/10.5530/ijper.51.1.6openalex-snapshot
DUSR (Distributed Ultrafast Shape Recognition): a Hadoop Based Tool to Identify Similar Shaped Ligand Molecules
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