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Assessing Scoring Functions for Protein−Ligand Interactions
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Outgoing claims: the papers this work cites, builds on, or argues with.
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Critical evaluation of search algorithms for automated molecular docking and database screening
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Ligand solvation in molecular docking
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Reviews in Computational Chemistry
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pH‐Dependent Binding Modes Observed in Trypsin Crystals: Lessons for Structure‐Based Drug Design
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ICM—A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation
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A Model Binding Site for Testing Scoring Functions in Molecular Docking
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What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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Using Active Site Mapping and Receptor-Based Pharmacophore Tools: Prelude to Docking and De Novo/Fragment-Based Ligand Design
inferred← citeshttps://doi.org/10.1007/978-1-61779-334-9_19openalex-snapshot
In Silico-Screening Approaches for Lead Generation: Identification of Novel Allosteric Modulators of Human-Erythrocyte Pyruvate Kinase
inferred← citeshttps://doi.org/10.1007/978-1-61779-465-0_19openalex-snapshot
The Solvated Interaction Energy Method for Scoring Binding Affinities
inferred← citeshttps://doi.org/10.1007/978-1-62703-342-8_1openalex-snapshot
Virtual Screening in Drug Design
inferred← citeshttps://doi.org/10.1007/978-1-62703-398-5_1openalex-snapshot
Protein–Ligand Interactions: Fundamentals
inferred← citeshttps://doi.org/10.1007/978-3-030-05282-9_5openalex-snapshot
In Silico Structure-Based Prediction of Receptor–Ligand Binding Affinity: Current Progress and Challenges
inferred← citeshttps://doi.org/10.1007/978-3-030-95895-4_1openalex-snapshot
Drug Discovery Paradigms: Target-Based Drug Discovery
inferred← citeshttps://doi.org/10.1007/978-3-031-72359-9_6openalex-snapshot
Target-Aware Drug Activity Model: A Deep Learning Approach to Virtual HTS
inferred← citeshttps://doi.org/10.1007/978-3-319-28495-8_9openalex-snapshot
Classifying Calpain Inhibitors for the Treatment of Cataracts: A Self Organising Map (SOM) ANN/KM Approach in Drug Discovery
inferred← citeshttps://doi.org/10.1007/978-3-319-50042-3_4openalex-snapshot
In Silico ADME Techniques Used in Early-Phase Drug Discovery
inferred← citeshttps://doi.org/10.1007/978-3-642-19615-7_16openalex-snapshot
Virtual screening by molecular docking
inferred← citeshttps://doi.org/10.1007/978-90-481-2368-1_2openalex-snapshot
Complementarity of Hydrophobic/Hydrophilic Properties In Protein—Ligand Complexes: A New Tool to Improve Docking Results
inferred← citeshttps://doi.org/10.1007/978-90-481-3034-4_16openalex-snapshot
Challenges for Computer Simulations in Drug Design
inferred← citeshttps://doi.org/10.1007/s00018-004-4422-3openalex-snapshot
Binding site of activators of the cystic fibrosis transmembrane conductance regulator in the nucleotide binding domains
inferred← citeshttps://doi.org/10.1007/s00044-013-0771-5openalex-snapshot
QSAR studies on diclofenac analogues as potent cyclooxygenase inhibitors using CoMFA and CoMSIA
inferred← citeshttps://doi.org/10.1007/s00894-004-0201-1openalex-snapshot
ProPose: a docking engine based on a fully configurable protein–ligand interaction model
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/s00894-012-1416-1openalex-snapshot
FDA approved drugs complexed to their targets: evaluating pose prediction accuracy of docking protocols
inferred← citeshttps://doi.org/10.1007/s00894-013-1821-0openalex-snapshot
Retrospective molecular docking study of WY-25105 ligand to β-secretase and bias of the three-dimensional structure flexibility
inferred← citeshttps://doi.org/10.1007/s00894-014-2251-3openalex-snapshot
A comparison of various optimization algorithms of protein–ligand docking programs by fitness accuracy
inferred← citeshttps://doi.org/10.1007/s00894-015-2834-7openalex-snapshot
Improving protein-ligand docking with flexible interfacial water molecules using SWRosettaLigand
inferred← citeshttps://doi.org/10.1007/s10340-025-01974-3openalex-snapshot
A novel monocarbonyl curcumin analog synergizes pesticide efficiency via cytochrome P450 inhibition in the whitefly Bemisia tabaci
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/s10822-005-8483-7openalex-snapshot
Scoring Functions – the First 100 Years
inferred← citeshttps://doi.org/10.1007/s10822-006-9043-5openalex-snapshot
Discovering New Classes of Brugia malayi Asparaginyl-tRNA Synthetase Inhibitors and Relating Specificity to Conformational Change
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/s10822-008-9189-4openalex-snapshot
Community benchmarks for virtual screening
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/s10822-009-9317-9openalex-snapshot
Docking flexible ligands in proteins with a solvent exposure- and distance-dependent dielectric function
inferred← citeshttps://doi.org/10.1007/s10822-010-9320-1openalex-snapshot
Screening of benzamidine-based thrombin inhibitors via a linear interaction energy in continuum electrostatics model
inferred← citeshttps://doi.org/10.1007/s10822-011-9482-5openalex-snapshot
Improving molecular docking through eHiTS’ tunable scoring function
inferred← citeshttps://doi.org/10.1007/s10822-011-9529-7openalex-snapshot
Exhaustive search and solvated interaction energy (SIE) for virtual screening and affinity prediction
inferred← citeshttps://doi.org/10.1007/s10822-012-9590-xopenalex-snapshot
Virtual fragment screening: exploration of MM-PBSA re-scoring
inferred← citeshttps://doi.org/10.1007/s10822-014-9715-5openalex-snapshot
Exhaustive docking and solvated interaction energy scoring: lessons learned from the SAMPL4 challenge
inferred← citeshttps://doi.org/10.1007/s10822-014-9794-3openalex-snapshot
Exploring the free-energy landscape of carbohydrate–protein complexes: development and validation of scoring functions considering the binding-site topology
inferred← citeshttps://doi.org/10.1007/s10822-015-9870-3openalex-snapshot
Ultrafast protein structure-based virtual screening with Panther
inferred← citeshttps://doi.org/10.1007/s10822-016-9917-0openalex-snapshot
Rapid activity prediction of HIV-1 integrase inhibitors: harnessing docking energetic components for empirical scoring by chemometric and artificial neural network approaches
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/s10822-018-0100-7openalex-snapshot
Enabling the hypothesis-driven prioritization of ligand candidates in big databases: Screenlamp and its application to GPCR inhibitor discovery for invasive species control
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/s10822-025-00638-9openalex-snapshot
Design, synthesis, characterization, in silico, in vitro and in vivo antidiabetic studies of novel benzothiophene derivatives
inferred← citeshttps://doi.org/10.1007/s10847-013-0363-5openalex-snapshot
3D-QSAR and docking studies of the stability constants of different guest molecules with beta-cyclodextrin
inferred← citeshttps://doi.org/10.1007/s13738-020-01913-2openalex-snapshot
Molecular docking studies and synthesis of a new class of chroman-4-one fused 1,3,4-thiadiazole derivatives and evaluation for their anticancer potential
inferred← citeshttps://doi.org/10.1007/s42250-025-01324-xopenalex-snapshot
In Silico Discovery and Screening of Small Molecule Inhibitors Targeting Glyceraldehyde-3-Phosphate Dehydrogenase ~ Triosephosphate Isomerase Protein Complex Towards New Anti-Schistosomal Drug Development
inferred← citeshttps://doi.org/10.1007/s44371-025-00346-1openalex-snapshot
In vivo and in silico evaluation of anxiolytic, antidepressant and cognitive enhancing activities of Maesa chisia leaves
inferred← citeshttps://doi.org/10.1007/s44395-025-00026-0openalex-snapshot
Discovering natural product inhibitors of Cryptococcus neoformans farnesyltransferase through data-fusion based screening and molecular dynamics
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/b978-0-12-816125-8.00004-3openalex-snapshot
Computational Drug Repurposing for Neurodegenerative Diseases
inferred← citeshttps://doi.org/10.1016/b978-0-12-821748-1.00001-4openalex-snapshot
Impact of chemoinformatics approaches and tools on current chemical research
inferred← citeshttps://doi.org/10.1016/b978-0-12-822248-5.00012-7openalex-snapshot
Virtual screening techniques in pharmaceutical research
inferred← citeshttps://doi.org/10.1016/b978-0-323-85700-0.00003-4openalex-snapshot
Natural polymers and hydrocolloids application in food
inferred← citeshttps://doi.org/10.1016/b978-0-443-29808-0.00016-9openalex-snapshot
Molecular docking—A solved problem?
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.2007.07.032openalex-snapshot
Inhibition of CYP2B4 by 2-ethynylnaphthalene: Evidence for the co-binding of substrate and inhibitor within the active site
inferred← citeshttps://doi.org/10.1016/j.abb.2015.05.011openalex-snapshot
Receptor-based virtual screening protocol for drug discovery
inferred← citeshttps://doi.org/10.1016/j.addr.2015.04.020openalex-snapshot
Prediction of cytochrome P450 mediated metabolism
inferred← citeshttps://doi.org/10.1016/j.asoc.2014.10.008openalex-snapshot
Adaptive molecular docking method based on information entropy genetic algorithm
inferred← citeshttps://doi.org/10.1016/j.bmc.2005.02.057openalex-snapshot
Connecting traditional QSAR and molecular simulations of papain hydrolysis—importance of charge transfer
inferred← citeshttps://doi.org/10.1016/j.bmc.2005.06.009openalex-snapshot
DFT-based ranking of zinc-binding groups in histone deacetylase inhibitors
inferred← citeshttps://doi.org/10.1016/j.bmc.2008.06.008openalex-snapshot
Characterization of the PON1 active site using modeling simulation, in relation to PON1 lactonase activity
inferred← citeshttps://doi.org/10.1016/j.bmc.2015.01.001openalex-snapshot
Discovery of Mer kinase inhibitors by virtual screening using Structural Protein–Ligand Interaction Fingerprints
inferred← citeshttps://doi.org/10.1016/j.bmcl.2013.10.044openalex-snapshot
Comprehending renin inhibitor’s binding affinity using structure-based approaches
inferred← citeshttps://doi.org/10.1016/j.bpc.2008.05.003openalex-snapshot
Solution 1H NMR study of the active site structure for the double mutant H64Q/V68F cyanide complex from mouse neuroglobin
inferred← citeshttps://doi.org/10.1016/j.bpj.2009.11.018openalex-snapshot
Accounting for Ligand Conformational Restriction in Calculations of Protein-Ligand Binding Affinities
inferred← citeshttps://doi.org/10.1016/j.bpj.2010.02.034openalex-snapshot
Improved Ligand-Protein Binding Affinity Predictions Using Multiple Binding Modes
inferred← citeshttps://doi.org/10.1016/j.compbiomed.2012.05.001openalex-snapshot
A scalable and accurate method for classifying protein–ligand binding geometries using a MapReduce approach
inferred← citeshttps://doi.org/10.1016/j.dcmed.2022.10.003openalex-snapshot
Exploring the phytoconstituents targeting TNF-α as potential lead compounds to treat inflammatory diseases: an in-silico approach
inferred← citeshttps://doi.org/10.1016/j.ddtec.2004.08.004openalex-snapshot
Scoring functions for protein–ligand interactions: a critical perspective
inferred← citeshttps://doi.org/10.1016/j.ddtec.2004.10.010openalex-snapshot
Lead identification in post-genomics: computers as a complementary alternative
inferred← citeshttps://doi.org/10.1016/j.drudis.2006.05.012openalex-snapshot
Virtual ligand screening: strategies, perspectives and limitations
inferred← citeshttps://doi.org/10.1016/j.drudis.2009.01.012openalex-snapshot
Healthy skepticism: assessing realistic model performance
inferred← citeshttps://doi.org/10.1016/j.ejmech.2006.12.037openalex-snapshot
The consequences of scoring docked ligand conformations using free energy correlations
inferred← citeshttps://doi.org/10.1016/j.ejmech.2009.06.011openalex-snapshot
Scoring function for DNA–drug docking of anticancer and antiparasitic compounds based on spectral moments of 2D lattice graphs for molecular dynamics trajectories
inferred← citeshttps://doi.org/10.1016/j.ejmech.2013.02.015openalex-snapshot
Molecular determinants for nuclear receptors selectivity: Chemometric analysis, dockings and site-directed mutagenesis of dual peroxisome proliferator-activated receptors α/γ agonists
inferred← citeshttps://doi.org/10.1016/j.ejmech.2015.09.024openalex-snapshot
Mutational mapping of the transmembrane binding site of the G-protein coupled receptor TGR5 and binding mode prediction of TGR5 agonists
inferred← citeshttps://doi.org/10.1016/j.febslet.2005.10.031openalex-snapshot
An all atom energy based computational protocol for predicting binding affinities of protein–ligand complexes
inferred← citeshttps://doi.org/10.1016/j.ica.2023.121598openalex-snapshot
Pt(IV) and Au(III) complexes with tridentate-benzothiazole based ligand: synthesis, characterization, biological applications (antibacterial, antifungal, antioxidant, anticancer and molecular docking) and DFT calculation
inferred← citeshttps://doi.org/10.1016/j.ijbiomac.2018.07.145openalex-snapshot
Inhibiting effects of common trivalent metal ions on transmembrane-type 2 matrix metalloproteinase
inferred← citeshttps://doi.org/10.1016/j.ijbiomac.2019.01.209openalex-snapshot
Disorder-to-helix conformational conversion of the human immunomodulatory peptide LL-37 induced by antiinflammatory drugs, food dyes and some metabolites
inferred← citeshttps://doi.org/10.1016/j.indcrop.2020.112207openalex-snapshot
Plectranthus barbatus Andrews as anti-Helicobacter pylori agent with activity against adenocarcinoma gastric cells
inferred← citeshttps://doi.org/10.1016/j.jiec.2019.12.009openalex-snapshot
Effect of ligand torsion number on the AutoDock mediated prediction of protein-ligand binding affinity
inferred← citeshttps://doi.org/10.1016/j.jmb.2006.01.034openalex-snapshot
Probing Molecular Docking in a Charged Model Binding Site
inferred← citeshttps://doi.org/10.1016/j.jmb.2008.09.073openalex-snapshot
The Thermodynamics of Protein–Ligand Interaction and Solvation: Insights for Ligand Design
inferred← citeshttps://doi.org/10.1016/j.jmgm.2015.01.009openalex-snapshot
Comparing sixteen scoring functions for predicting biological activities of ligands for protein targets
inferred← citeshttps://doi.org/10.1016/j.jmgm.2016.06.008openalex-snapshot
Binding affinity models for Falcipain inhibition based on the Linear Interaction Energy method
inferred← citeshttps://doi.org/10.1016/j.jmgm.2017.02.010openalex-snapshot
Combined Monte Carlo/torsion-angle molecular dynamics for ensemble modeling of proteins, nucleic acids and carbohydrates
inferred← citeshttps://doi.org/10.1016/j.jmgm.2017.10.021openalex-snapshot
FLIP: An assisting software in structure based drug design using fingerprint of protein-ligand interaction profiles
inferred← citeshttps://doi.org/10.1016/j.jmgm.2019.03.003openalex-snapshot
In silico profiling the interaction mechanism of 2,5-diketopiperazine derivatives as oxytocin antagonists
inferred← citeshttps://doi.org/10.1016/j.jmgm.2025.109272openalex-snapshot
Computational modeling of ubiquitin specific protease 7 (USP7) complexes with N-benzylpiperidinol derivatives incorporating binding site flexibility
inferred← citeshttps://doi.org/10.1016/j.jsb.2005.11.003openalex-snapshot
Molecular insight into pseudolysin inhibition using the MM-PBSA and LIE methods
inferred← citeshttps://doi.org/10.1016/j.molstruc.2026.146876openalex-snapshot
Pyrimidine-based HER2 inhibitors: Design, synthesis, biological evaluation, and molecular modeling for breast cancer therapy
inferred← citeshttps://doi.org/10.1016/j.parco.2017.02.005openalex-snapshot
Enabling scalable and accurate clustering of distributed ligand geometries on supercomputers
inferred← citeshttps://doi.org/10.1016/j.polymer.2009.05.055openalex-snapshot
Study of peptide fingerprints of parasite proteins and drug–DNA interactions with Markov-Mean-Energy invariants of biopolymer molecular-dynamic lattice networks
inferred← citeshttps://doi.org/10.1016/j.sbi.2004.03.009openalex-snapshot
Recent advances in the development and application of implicit solvent models in biomolecule simulations
inferred← citeshttps://doi.org/10.1016/j.sciaf.2025.e02692openalex-snapshot
Unveiling novel VEGFR-2 inhibitors: QSAR modeling, molecular docking, MD and MM-GBSA calculations, pharmacokinetics profiling and DFT studies
inferred← citeshttps://doi.org/10.1016/j.semcancer.2020.04.007openalex-snapshot
Rational drug repurposing for cancer by inclusion of the unbiased molecular dynamics simulation in the structure-based virtual screening approach: Challenges and breakthroughs
inferred← citeshttps://doi.org/10.1016/j.str.2009.02.010openalex-snapshot
Binding of Small-Molecule Ligands to Proteins: “What You See” Is Not Always “What You Get”
inferred← citeshttps://doi.org/10.1016/j.vascn.2010.02.005openalex-snapshot
Troubleshooting computational methods in drug discovery
inferred← citeshttps://doi.org/10.1016/j.yexmp.2022.104849openalex-snapshot
Docking is not enough: 17-trifluoromethylphenyl trinor PGF2α is only a very weak ligand of neurokinin-1 receptor
inferred← citeshttps://doi.org/10.1016/j.ymeth.2014.08.001openalex-snapshot
Virtual screening: An in silico tool for interlacing the chemical universe with the proteome
inferred← citeshttps://doi.org/10.1016/j.ymeth.2014.11.015openalex-snapshot
Benchmarking methods and data sets for ligand enrichment assessment in virtual screening
inferred← citeshttps://doi.org/10.1016/s0065-3233(05)72007-6openalex-snapshot
Peptide and Protein Folding and Conformational Equilibria: Theoretical Treatment of Electrostatics and Hydrogen Bonding with Implicit Solvent Models
inferred← citeshttps://doi.org/10.1016/s0079-6468(05)44401-xopenalex-snapshot
1 Finding Protein Kinase Hits using Structural Information
inferred← citeshttps://doi.org/10.1017/cbo9780511730412.007openalex-snapshot
Free-energy calculations in structure-based drug design
inferred← citeshttps://doi.org/10.1021/acs.biochem.6b00217openalex-snapshot
Computational Analysis of Sterol Ligand Specificity of the Niemann Pick C2 Protein
inferred← citeshttps://doi.org/10.1021/acs.chemrev.5b00583openalex-snapshot
Experimental Binding Energies in Supramolecular Complexes
inferred← citeshttps://doi.org/10.1021/acs.jcim.1c01061openalex-snapshot
Modeling the Structure–Activity Relationship of Arbidol Derivatives and Other SARS-CoV-2 Fusion Inhibitors Targeting the S2 Segment of the Spike Protein
inferred← citeshttps://doi.org/10.1021/acs.jcim.2c00485openalex-snapshot
Delta Machine Learning to Improve Scoring-Ranking-Screening Performances of Protein–Ligand Scoring Functions
inferred← citeshttps://doi.org/10.1021/acs.jcim.2c01531openalex-snapshot
Activity Models of Key GPCR Families in the Central Nervous System: A Tool for Many Purposes
inferred← citeshttps://doi.org/10.1021/acs.jcim.5b00704openalex-snapshot
Solution-Binding and Molecular Docking Approaches Combine to Provide an Expanded View of Multidrug Recognition in the MDR Gene Regulator BmrR
inferred← citeshttps://doi.org/10.1021/acs.jcim.6b00373openalex-snapshot
Efficient Approximation of Ligand Rotational and Translational Entropy Changes upon Binding for Use in MM-PBSA Calculations
inferred← citeshttps://doi.org/10.1021/acs.jcim.6b00418openalex-snapshot
Evaluation of Generalized Born Models for Large Scale Affinity Prediction of Cyclodextrin Host–Guest Complexes
inferred← citeshttps://doi.org/10.1021/acs.jcim.8b00582openalex-snapshot
Converging a Knowledge-Based Scoring Function: DrugScore2018
inferred← citeshttps://doi.org/10.1021/acs.jcim.9b00645openalex-snapshot
Incorporating Explicit Water Molecules and Ligand Conformation Stability in Machine-Learning Scoring Functions
inferred← citeshttps://doi.org/10.1021/acschemneuro.6b00216openalex-snapshot
Multistep Modeling Strategy To Improve the Binding Affinity Prediction of PET Tracers to Aβ42: Case Study with Styrylbenzoxazole Derivatives
inferred← citeshttps://doi.org/10.1021/bi0616100openalex-snapshot
The Role of Loop F Residues in Determining Differentiald-Tubocurarine Potencies in Mouse and Human 5-Hydroxytryptamine 3A Receptors
inferred← citeshttps://doi.org/10.1021/bi062320mopenalex-snapshot
Ensemble Modeling of Substrate Binding to Cytochromes P450: Analysis of Catalytic Differences between CYP1A Orthologs,
inferred← citeshttps://doi.org/10.1021/bi2004558openalex-snapshot
Efficient Incorporation of Protein Flexibility and Dynamics into Molecular Docking Simulations
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