On the public citation graph
On Evaluating Molecular-Docking Methods for Pose Prediction and Enrichment Factors
0 signed · 262 inferred · view as graph
Inferred edges come from two machine sources: sweeps of open repository metadata (mostly SSRN and Zenodo), and a bulk OpenAlex citation snapshot. Every row below is labelled with the one it came from. Neither is a complete citation index — absence here is not evidence of absence.
Is this your work? Sign in with ORCID and put your name on the
claims that are yours.
Reference health. See whether every reference in this work resolves to a
known work and none has been retracted — and get a dated CiteStamped
badge you can embed.
What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1002/(sici)1096-987x(199604)17:5/6<490::aid-jcc1>3.0.co;2-popenalex-snapshot
Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94
inferredcites →https://doi.org/10.1002/(sici)1096-987x(19971115)18:14<1812::aid-jcc10>3.0.co;2-hopenalex-snapshot
Automated flexible ligand docking method and its application for database search
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)1097-0134(19991101)37:2<228::aid-prot8>3.0.co;2-8openalex-snapshot
Evaluation of the FLEXX incremental construction algorithm for protein-ligand docking
inferredcites →https://doi.org/10.1002/jcc.540130608openalex-snapshot
Conformational analysis of flexible ligands in macromolecular receptor sites
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/jmr.300060305openalex-snapshot
A novel computational tool for automated structure‐based drug design
inferredcites →https://doi.org/10.1002/prot.20149openalex-snapshot
Comparative evaluation of eight docking tools for docking and virtual screening accuracy
inferredcites →https://doi.org/10.1002/prot.20497openalex-snapshot
Comparing protein–ligand docking programs is difficult
inferredcites →https://doi.org/10.1006/jcph.1999.6233openalex-snapshot
Ab InitioFolding of Peptides by the Optimal-Bias Monte Carlo Minimization Procedure
inferredcites →https://doi.org/10.1006/jmbi.1994.1052openalex-snapshot
Biased Probability Monte Carlo Conformational Searches and Electrostatic Calculations for Peptides and Proteins
inferredcites →https://doi.org/10.1006/jmbi.1996.0477openalex-snapshot
A Fast Flexible Docking Method using an Incremental Construction Algorithm
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/10.1006/jmbi.1999.3371openalex-snapshot
Knowledge-based scoring function to predict protein-ligand interactions
inferredcites →https://doi.org/10.1007/bf00124324openalex-snapshot
A genetic algorithm for flexible molecular overlay and pharmacophore elucidation
inferredcites →https://doi.org/10.1016/0022-2836(92)90936-eopenalex-snapshot
Optimal protocol and trajectory visualization for conformational searches of peptides and proteins
inferredcites →https://doi.org/10.1016/0898-5529(90)90156-3openalex-snapshot
Automatic generation of 3D-atomic coordinates for organic molecules
inferredcites →https://doi.org/10.1016/s1359-6446(01)02091-8openalex-snapshot
Virtual screening and fast automated docking methods
inferredcites →https://doi.org/10.1016/s1359-6446(02)02289-4openalex-snapshot
Genome annotation techniques: new approaches and challenges
inferredcites →https://doi.org/10.1016/s1367-5931(00)00217-9openalex-snapshot
High-throughput docking for lead generation
inferredcites →https://doi.org/10.1016/s1367-5931(02)00339-3openalex-snapshot
Lead discovery using molecular docking
inferredcites →https://doi.org/10.1016/s1741-8364(04)02417-5openalex-snapshot
Assessing the impact of high-performance computing on the drug discovery and development process
inferredcites →https://doi.org/10.1021/ci00002a004openalex-snapshot
The development of versions 3 and 4 of the Cambridge Structural Database System
inferredcites →https://doi.org/10.1021/ci00002a005openalex-snapshot
Chemical Abstracts Service Chemical Registry System. 13. Enhanced handling of stereochemistry
inferredcites →https://doi.org/10.1021/ci049970mopenalex-snapshot
Assessment of Docking Poses: Interactions-Based Accuracy Classification (IBAC) versus Crystal Structure Deviations
inferredcites →https://doi.org/10.1021/j100194a068openalex-snapshot
Energy parameters in polypeptides. 10. Improved geometrical parameters and nonbonded interactions for use in the ECEPP/3 algorithm, with application to proline-containing peptides
inferredcites →https://doi.org/10.1021/j100194a069openalex-snapshot
A Gibbs-Donnan-based interpretation of the sensitivity of the measurable acid dissociation properties of poly(acrylic acid) to concentration levels of salt and polyelectrolyte
inferredcites →https://doi.org/10.1021/jm0003992openalex-snapshot
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
inferredcites →https://doi.org/10.1021/jm0302997openalex-snapshot
Evaluation of Docking Performance: Comparative Data on Docking Algorithms
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/jm049798dopenalex-snapshot
Comparison of Automated Docking Programs as Virtual Screening Tools
inferredcites →https://doi.org/10.1023/a:1007907728892openalex-snapshot
QXP: Powerful, rapid computer algorithms for structure-based drug design
inferredcites →https://doi.org/10.1023/a:1007996124545openalex-snapshot
Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes
inferredcites →https://doi.org/10.1023/b:jcam.0000017496.76572.6fopenalex-snapshot
Comparative study of several algorithms for flexible ligand docking
inferredcites →https://doi.org/10.1038/nrd1129openalex-snapshot
Implications of protein flexibility for drug discovery
inferredcites →https://doi.org/10.1038/nrd941openalex-snapshot
Integration of virtual and high-throughput screening
inferredcites →https://doi.org/10.1063/1.1699114openalex-snapshot
Equation of State Calculations by Fast Computing Machines
inferredcites →https://doi.org/10.1074/mcp.m400159-mcp200openalex-snapshot
Pocketome via Comprehensive Identification and Classification of Ligand Binding Envelopes
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1002/9783527806539.ch6hopenalex-snapshot
Structure‐Based Virtual Screening
inferred← citeshttps://doi.org/10.1002/9783527840748.ch20openalex-snapshot
Community Benchmarking Exercises for Docking and Scoring
inferred← citeshttps://doi.org/10.1002/ardp.200800042openalex-snapshot
Refined Docking as a Valuable Tool for Lead Optimization: Application to Histamine H3 Receptor Antagonists
inferred← citeshttps://doi.org/10.1002/ardp.201300118openalex-snapshot
Synthesis of Sydnone Substituted Biginelli Derivatives as Hyaluronidase Inhibitors
inferred← citeshttps://doi.org/10.1002/biot.200700259openalex-snapshot
Computational chemistry approaches to drug discovery in signal transduction
inferred← citeshttps://doi.org/10.1002/cem.1367openalex-snapshot
Multivariate assessment of virtual screening experiments
inferred← citeshttps://doi.org/10.1002/cphc.202400653openalex-snapshot
Evaluating Quinolines: Molecular Dynamics Approach to Assess Their Potential as Acetylcholinesterase Inhibitors for Alzheimer's Disease.
inferred← citeshttps://doi.org/10.1002/jcc.20770openalex-snapshot
Shapelets: Possibilities and limitations of shape‐based virtual screening
inferred← citeshttps://doi.org/10.1002/jcc.21395openalex-snapshot
Q‐DockLHM: Low‐resolution refinement for ligand comparative modeling
inferred← citeshttps://doi.org/10.1002/jcc.21409openalex-snapshot
Exploring hierarchical refinement techniques for induced fit docking with protein and ligand flexibility
inferred← citeshttps://doi.org/10.1002/jcc.21498openalex-snapshot
Evaluation of the performance of four molecular docking programs on a diverse set of protein‐ligand complexes
inferred← citeshttps://doi.org/10.1002/jcc.21642openalex-snapshot
VoteDock: Consensus docking method for prediction of protein–ligand interactions
inferred← citeshttps://doi.org/10.1002/jcc.21643openalex-snapshot
Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database
inferred← citeshttps://doi.org/10.1002/minf.201300143openalex-snapshot
eFindSite: Enhanced Fingerprint‐Based Virtual Screening Against Predicted Ligand Binding Sites in Protein Models
inferred← citeshttps://doi.org/10.1002/minf.202100178openalex-snapshot
Development of a Novel Pharmacophore Model Guided by the Ensemble of Waters and Small Molecule Fragments Bound to SARS‐CoV‐2 Main Protease
inferred← citeshttps://doi.org/10.1002/prot.21082openalex-snapshot
Protein–ligand docking: Current status and future challenges
inferred← citeshttps://doi.org/10.1002/prot.21367openalex-snapshot
EADock: Docking of small molecules into protein active sites with a multiobjective evolutionary optimization
inferred← citeshttps://doi.org/10.1002/prot.21405openalex-snapshot
Structure‐based virtual ligand screening with LigandFit: Pose prediction and enrichment of compound collections
inferred← citeshttps://doi.org/10.1002/prot.21841openalex-snapshot
In meso crystal structure and docking simulations suggest an alternative proteoglycan binding site in the OpcA outer membrane adhesin
inferred← citeshttps://doi.org/10.1002/prot.22415openalex-snapshot
Automated site preparation in physics‐based rescoring of receptor ligand complexes
inferred← citeshttps://doi.org/10.1002/prot.23173openalex-snapshot
The interprotein scoring noises in glide docking scores
inferred← citeshttps://doi.org/10.1007/128_2011_213openalex-snapshot
Application of NMR and Molecular Docking in Structure-Based Drug Discovery
inferred← citeshttps://doi.org/10.1007/7355_2021_130openalex-snapshot
Ligand- and Structure-Based Virtual Screening in Drug Discovery
inferred← citeshttps://doi.org/10.1007/978-1-0716-3311-3_8openalex-snapshot
Recent Advances in Computational Modeling of Multi-targeting Inhibitors as Anti-Alzheimer Agents
inferred← citeshttps://doi.org/10.1007/978-1-4939-9504-2_5openalex-snapshot
Computational Opportunities and Challenges in Finding Cyclic Peptide Modulators of Protein–Protein Interactions
inferred← citeshttps://doi.org/10.1007/978-1-61779-520-6_9openalex-snapshot
Leveraging Structural Information for the Discovery of New Drugs: Computational Methods
inferred← citeshttps://doi.org/10.1007/978-1-61779-588-6_16openalex-snapshot
Preparation and Refinement of Model Protein–Ligand Complexes
inferred← citeshttps://doi.org/10.1007/978-1-62703-017-5_13openalex-snapshot
Molecular Docking Methodologies
inferred← citeshttps://doi.org/10.1007/978-3-031-75457-9_1openalex-snapshot
Quantitative Structure Interaction Activity Relationship (QSIAR) as a Novel Approach to Drug Design: A Case Study of Anti-tubercular Agents
inferred← citeshttps://doi.org/10.1007/978-3-211-75123-7_17openalex-snapshot
Protein-protein interactions: analysis and prediction
inferred← citeshttps://doi.org/10.1007/s00044-016-1707-7openalex-snapshot
Design and anti-HIV activity of arylsulphonamides as non-nucleoside reverse transcriptase inhibitors
inferred← citeshttps://doi.org/10.1007/s00217-017-2946-7openalex-snapshot
Thrombin inhibitory peptides derived from Mytilus edulis proteins: identification, molecular docking and in silico prediction of toxicity
inferred← citeshttps://doi.org/10.1007/s00706-016-1674-1openalex-snapshot
Comparing pharmacophore models derived from crystal structures and from molecular dynamics simulations
inferred← citeshttps://doi.org/10.1007/s00894-010-0817-2openalex-snapshot
Docking and 3D-QSAR modeling of cyclin-dependent kinase 5/p25 inhibitors
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/s10439-012-0576-6openalex-snapshot
Structural Systems Biology and Multiscale Signaling Models
inferred← citeshttps://doi.org/10.1007/s10822-007-9138-7openalex-snapshot
Discovery of small molecule inhibitors of ubiquitin-like poxvirus proteinase I7L using homology modeling and covalent docking approaches
inferred← citeshttps://doi.org/10.1007/s10822-007-9163-6openalex-snapshot
Evaluation of the performance of 3D virtual screening protocols: RMSD comparisons, enrichment assessments, and decoy selection—What can we learn from earlier mistakes?
inferred← citeshttps://doi.org/10.1007/s10822-007-9167-2openalex-snapshot
Optimization of CAMD techniques 3. Virtual screening enrichment studies: a help or hindrance in tool selection?
inferred← citeshttps://doi.org/10.1007/s10822-008-9169-8openalex-snapshot
Evaluating docking programs: keeping the playing field level
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/s10822-008-9258-8openalex-snapshot
Scoring confidence index: statistical evaluation of ligand binding mode predictions
inferred← citeshttps://doi.org/10.1007/s10822-009-9281-4openalex-snapshot
Virtual fragment screening: an exploration of various docking and scoring protocols for fragments using Glide
inferred← citeshttps://doi.org/10.1007/s10822-019-00276-yopenalex-snapshot
Druggable exosites of the human kino-pocketome
inferred← citeshttps://doi.org/10.1007/s10822-025-00706-0openalex-snapshot
Molecular simulation-based 3D structural construction of olfactory receptor with agonist binding
inferred← citeshttps://doi.org/10.1007/s10822-026-00763-zopenalex-snapshot
Mechanistic insights into the noncovalent inhibition of SARS-CoV-2 PLpro: a multiscale computational study
inferred← citeshttps://doi.org/10.1007/s10822-026-00764-yopenalex-snapshot
The discovery of monoamine oxidase inhibitors: virtual screening and in vitro inhibition potencies
inferred← citeshttps://doi.org/10.1007/s12551-016-0247-1openalex-snapshot
Software for molecular docking: a review
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/b978-0-443-29808-0.00016-9openalex-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.2008.12.013openalex-snapshot
The X-ray structure of ricin A chain with a novel inhibitor
inferred← citeshttps://doi.org/10.1016/j.amc.2007.05.002openalex-snapshot
Use of genetic algorithms and solvation potential to study peptides structure
inferred← citeshttps://doi.org/10.1016/j.amc.2007.09.033openalex-snapshot
Using genetic algorithm to design protein sequence
inferred← citeshttps://doi.org/10.1016/j.amc.2007.09.038openalex-snapshot
Predicting peptides structure with solvation potential and rotamer library dependent of the backbone
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.bbamem.2023.184220openalex-snapshot
Repurposing dye ligands as antivirals via a docking approach on viral membrane and globular proteins – SARS-CoV-2 and HPV-16
inferred← citeshttps://doi.org/10.1016/j.biosystems.2007.11.004openalex-snapshot
Selection and flexible optimization of binding modes from conformation ensembles
inferred← citeshttps://doi.org/10.1016/j.bmc.2008.07.089openalex-snapshot
Synthesis, biological active molecular design, and molecular docking study of novel deazaflavin–cholestane hybrid compounds
inferred← citeshttps://doi.org/10.1016/j.bmc.2009.03.027openalex-snapshot
Combinatorial chemistry in the agrosciences
inferred← citeshttps://doi.org/10.1016/j.bmc.2018.05.015openalex-snapshot
Molecular modeling, synthesis, antibacterial and cytotoxicity evaluation of sulfonamide derivatives of benzimidazole, indazole, benzothiazole and thiazole
inferred← citeshttps://doi.org/10.1016/j.bmcl.2007.11.107openalex-snapshot
Inhibition of dipeptidyl peptidase-IV (DPP-IV) by atorvastatin
inferred← citeshttps://doi.org/10.1016/j.bmcl.2009.08.042openalex-snapshot
Structure based virtual screening of GSK-3β: Importance of protein flexibility and induced fit
inferred← citeshttps://doi.org/10.1016/j.bpj.2018.09.021openalex-snapshot
Mapping the Ligand Binding Landscape
inferred← citeshttps://doi.org/10.1016/j.cbi.2015.03.023openalex-snapshot
In silico and biological analysis of anti-androgen activity of the brominated flame retardants ATE, BATE and DPTE in zebrafish
inferred← citeshttps://doi.org/10.1016/j.cbpa.2006.06.022openalex-snapshot
Streamlining lead discovery by aligning in silico and high-throughput screening
inferred← citeshttps://doi.org/10.1016/j.compbiolchem.2014.11.001openalex-snapshot
Docking assay of small molecule antivirals to p7 of HCV
inferred← citeshttps://doi.org/10.1016/j.compbiolchem.2016.04.010openalex-snapshot
Small molecule ligand docking to genotype specific bundle structures of hepatitis C virus (HCV) p7 protein
inferred← citeshttps://doi.org/10.1016/j.compbiolchem.2018.05.021openalex-snapshot
Synthesis, antibacterial activity, synergistic effect, cytotoxicity, docking and molecular dynamics of benzimidazole analogues
inferred← citeshttps://doi.org/10.1016/j.compbiolchem.2018.10.008openalex-snapshot
Synthesis, docking, ADMET prediction, cytotoxicity and antimicrobial activity of oxathiadiazole derivatives
inferred← citeshttps://doi.org/10.1016/j.compbiolchem.2020.107400openalex-snapshot
Alkylated benzimidazoles: Design, synthesis, docking, DFT analysis, ADMET property, molecular dynamics and activity against HIV and YFV
inferred← citeshttps://doi.org/10.1016/j.drudis.2007.12.002openalex-snapshot
Towards improving compound selection in structure-based virtual screening
inferred← citeshttps://doi.org/10.1016/j.ejmech.2006.12.028openalex-snapshot
In-silico drug screening method based on the protein–compound affinity matrix using the factor selection technique
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.2010.08.018openalex-snapshot
Novel structural insights for drug design of selective 5-HT2C inverse agonists from a ligand-biased receptor model
inferred← citeshttps://doi.org/10.1016/j.ejps.2020.105603openalex-snapshot
Methylene blue analogues: In vitro antimicrobial minimum inhibitory concentrations and in silico pharmacophore modelling
inferred← citeshttps://doi.org/10.1016/j.insi.2026.100438openalex-snapshot
Phytochemical modulation of inflammatory and oxidative pathways in rheumatoid arthritis: Insights from multi-omics and machine learning
inferred← citeshttps://doi.org/10.1016/j.jmb.2022.167637openalex-snapshot
An Electrostatically-steered Conformational Selection Mechanism Promotes SARS-CoV-2 Spike Protein Variation
inferred← citeshttps://doi.org/10.1016/j.jmb.2024.168540openalex-snapshot
CAPRI-Q: The CAPRI resource evaluating the quality of predicted structures of protein complexes
inferred← citeshttps://doi.org/10.1016/j.jmgm.2007.02.002openalex-snapshot
Combining docking, scoring and molecular field analyses to probe influenza neuraminidase–ligand interactions
inferred← citeshttps://doi.org/10.1016/j.jmgm.2007.11.003openalex-snapshot
Molecular docking/dynamics studies of Aurora A kinase inhibitors
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.2025.109076openalex-snapshot
Harnessing computational tools for drug discovery: An integrated computational approach to identify potential BACE-1 inhibitors
inferred← citeshttps://doi.org/10.1016/j.matpr.2020.10.377openalex-snapshot
Catalytic synthesis, spectral characterization, antimicrobial and molecular docking studies on some novel [E]-N-phenyl-3,5-dichloropyridin-4-amine and its derivatives
inferred← citeshttps://doi.org/10.1016/j.molstruc.2021.130763openalex-snapshot
Molecular modeling, QSAR analysis and antimicrobial properties of Schiff base derivatives of isatin
inferred← citeshttps://doi.org/10.1016/j.rechem.2023.100863openalex-snapshot
The pterin binding site of dihydropteroate synthase (DHPS): In silico screening and in vitro antibacterial activity of existing drugs
inferred← citeshttps://doi.org/10.1016/j.toxicon.2010.05.009openalex-snapshot
Identification of new classes of ricin toxin inhibitors by virtual screening
inferred← citeshttps://doi.org/10.1016/j.ymeth.2007.02.014openalex-snapshot
Strategies for developing protein tyrosine phosphatase inhibitors
inferred← citeshttps://doi.org/10.1016/s1574-1400(06)02016-0openalex-snapshot
Chapter 16 Recent Evaluations of High Throughput Docking Methods for Pharmaceutical Lead Finding – Consensus and Caveats
inferred← citeshttps://doi.org/10.1021/acs.jcim.4c01096openalex-snapshot
Evaluations of the Perturbation Resistance of the Deep-Learning-Based Ligand Conformation Optimization Algorithm
inferred← citeshttps://doi.org/10.1021/acs.jcim.5b00087openalex-snapshot
Three Homology Models of PAR2 Derived from Different Templates: Application to Antagonist Discovery
inferred← citeshttps://doi.org/10.1021/acs.jcim.5b00158openalex-snapshot
Accounting for Intraligand Interactions in Flexible Ligand Docking with a PMF-Based Scoring Function
inferred← citeshttps://doi.org/10.1021/acs.jcim.6c01611openalex-snapshot
Assessing the Generalizability of Machine Learning and Physics-Based Methods with DNA-Encoded Libraries
inferred← citeshttps://doi.org/10.1021/acs.jcim.7b00125openalex-snapshot
Modeling Binding with Large Conformational Changes: Key Points in Ensemble-Docking Approaches
inferred← citeshttps://doi.org/10.1021/acs.jctc.0c00752openalex-snapshot
Reversibly Sampling Conformations and Binding Modes Using Molecular Darting
inferred← citeshttps://doi.org/10.1021/acs.jpcb.2c03967openalex-snapshot
Mechanisms of Electron Transfer Rate Modulations in Cytochrome P450 BM3
inferred← citeshttps://doi.org/10.1021/acsmedchemlett.0c00540openalex-snapshot
Derivatization Design of Synthetically Accessible Space for Optimization: In Silico Synthesis vs Deep Generative Design
inferred← citeshttps://doi.org/10.1021/acsomega.0c00205openalex-snapshot
Homology Modeling of Human Uridine-5′-diphosphate-glucuronosyltransferase 1A6 Reveals Insights into Factors Influencing Substrate and Cosubstrate Binding
inferred← citeshttps://doi.org/10.1021/bk-2011-1076.ch006openalex-snapshot
A Fragment-Based Docking Engine: eHiTS
inferred← citeshttps://doi.org/10.1021/ci049612jopenalex-snapshot
Improved CoMFA Modeling by Optimization of Settings
inferred← citeshttps://doi.org/10.1021/ci100235nopenalex-snapshot
Comprehensive Structural and Functional Characterization of the Human Kinome by Protein Structure Modeling and Ligand Virtual Screening
inferred← citeshttps://doi.org/10.1021/ci200080gopenalex-snapshot
Construction and Test of Ligand Decoy Sets Using MDock: Community Structure–Activity Resource Benchmarks for Binding Mode Prediction
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/ci500080qopenalex-snapshot
Comparative Assessment of Scoring Functions on an Updated Benchmark: 1. Compilation of the Test Set
inferred← citeshttps://doi.org/10.1021/ci500081mopenalex-snapshot
Comparative Assessment of Scoring Functions on an Updated Benchmark: 2. Evaluation Methods and General Results
inferred← citeshttps://doi.org/10.1021/ci5001086openalex-snapshot
The Application of Statistical Methods to Cognate Docking: A Path Forward?
inferred← citeshttps://doi.org/10.1021/ci600342eopenalex-snapshot
Optimizing Fragment and Scaffold Docking by Use of Molecular Interaction Fingerprints
inferred← citeshttps://doi.org/10.1021/ci6005596openalex-snapshot
A Multivariate Approach to Investigate Docking Parameters' Effects on Docking Performance
inferred← citeshttps://doi.org/10.1021/ci700014hopenalex-snapshot
Conformational Coverage by a Genetic Algorithm: Saturation of Conformational Space
inferred← citeshttps://doi.org/10.1021/ci700031vopenalex-snapshot
MED-SuMoLig: A New Ligand-Based Screening Tool for Efficient Scaffold Hopping
inferred← citeshttps://doi.org/10.1021/ci7000378openalex-snapshot
Evaluations of Molecular Docking Programs for Virtual Screening
inferred← citeshttps://doi.org/10.1021/ci700052xopenalex-snapshot
Comparison of Topological, Shape, and Docking Methods in Virtual Screening
inferred← citeshttps://doi.org/10.1021/ci700216uopenalex-snapshot
FieldChopper, A New Tool for Automatic Model Generation and Virtual Screening Based on Molecular Fields
inferred← citeshttps://doi.org/10.1021/ci700253hopenalex-snapshot
Lessons in Molecular Recognition. 2. Assessing and Improving Cross-Docking Accuracy
inferred← citeshttps://doi.org/10.1021/ci7003169openalex-snapshot
On Evaluating Molecular-Docking Methods for Pose Prediction and Enrichment Factors. [J. Chem. Inf. Model. 46, 401−415 (2006)] by
inferred← citeshttps://doi.org/10.1021/ci700439zopenalex-snapshot
Exploiting Structure–Activity Relationships in Docking
inferred← citeshttps://doi.org/10.1021/ci7004548openalex-snapshot
AutoShim: Empirically Corrected Scoring Functions for Quantitative Docking with a Crystal Structure and IC50 Training Data
inferred← citeshttps://doi.org/10.1021/ci800084xopenalex-snapshot
An Alternative Method for the Evaluation of Docking Performance: RSR vs RMSD
inferred← citeshttps://doi.org/10.1021/ci800154wopenalex-snapshot
Evaluation of Different Virtual Screening Programs for Docking in a Charged Binding Pocket
inferred← citeshttps://doi.org/10.1021/ci800293nopenalex-snapshot
Validation of Molecular Docking Programs for Virtual Screening against Dihydropteroate Synthase
inferred← citeshttps://doi.org/10.1021/ci8003978openalex-snapshot
Better than Random? The Chemotype Enrichment Problem
inferred← citeshttps://doi.org/10.1021/ci8004176openalex-snapshot
Docking Ligands into Flexible and Solvated Macromolecules. 3. Impact of Input Ligand Conformation, Protein Flexibility, and Water Molecules on the Accuracy of Docking Programs
inferred← citeshttps://doi.org/10.1021/ci800432sopenalex-snapshot
Assessment of QM/MM Scoring Functions for Molecular Docking to HIV-1 Protease
inferred← citeshttps://doi.org/10.1021/ci9000053openalex-snapshot
Comparative Assessment of Scoring Functions on a Diverse Test Set
inferred← citeshttps://doi.org/10.1021/ci900199eopenalex-snapshot
Predicting Multiple Ligand Binding Modes Using Self-Consistent Pharmacophore Hypotheses
inferred← citeshttps://doi.org/10.1021/ci9004157openalex-snapshot
Accuracy Assessment of Protein-Based Docking Programs against RNA Targets
inferred← citeshttps://doi.org/10.1021/ci900498nopenalex-snapshot
HPPD: Ligand- and Target-Based Virtual Screening on a Herbicide Target
inferred← citeshttps://doi.org/10.1021/jm061277yopenalex-snapshot
Diverse, High-Quality Test Set for the Validation of Protein−Ligand Docking Performance
inferred← citeshttps://doi.org/10.1021/jm100442uopenalex-snapshot
The Pthaladyns: GTP Competitive Inhibitors of Dynamin I and II GTPase Derived from Virtual Screening
inferred← citeshttps://doi.org/10.1021/jm701248topenalex-snapshot
Docking Study Yields Four Novel Inhibitors of the Protooncogene Pim-1 Kinase
inferred← citeshttps://doi.org/10.1021/jm8008019openalex-snapshot
Discovery of Potent Thermolysin Inhibitors Using Structure Based Virtual Screening and Binding Assays
inferred← citeshttps://doi.org/10.1021/jm8010299openalex-snapshot
Type-II Kinase Inhibitor Docking, Screening, and Profiling Using Modified Structures of Active Kinase States
inferred← citeshttps://doi.org/10.1021/jm900414xopenalex-snapshot
One Scaffold, Three Binding Modes: Novel and Selective Pteridine Reductase 1 Inhibitors Derived from Fragment Hits Discovered by Virtual Screening
inferred← citeshttps://doi.org/10.1038/aps.2009.159openalex-snapshot
Pharmacophore-based virtual screening versus docking-based virtual screening: a benchmark comparison against eight targets
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/s41467-025-57852-0openalex-snapshot
RNAmigos2: accelerated structure-based RNA virtual screening with deep graph learning
inferred← citeshttps://doi.org/10.1038/s41929-026-01478-yopenalex-snapshot
A geometric foundation model for enzyme retrieval with evolutionary insights
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/10.1038/srep00323openalex-snapshot
How well do the substrates KISS the enzyme? Molecular docking program selection for feruloyl esterases
inferred← citeshttps://doi.org/10.1039/9781847558879-00076openalex-snapshot
Pharmacophore-based Virtual Screening in Drug Discovery
inferred← citeshttps://doi.org/10.1039/9781847558879-00295openalex-snapshot
Integrated Chemo- and Bioinformatics Approaches to Virtual Screening
inferred← citeshttps://doi.org/10.1039/c5mb00476dopenalex-snapshot
Recognizing drug targets using evolutionary information: implications for repurposing FDA-approved drugs against Mycobacterium tuberculosis H37Rv
inferred← citeshttps://doi.org/10.1039/d0nj02537bopenalex-snapshot
Combinatorial library generation, molecular docking and molecular dynamics simulations for enhancing the isoflavone scaffold in phosphodiesterase inhibition
inferred← citeshttps://doi.org/10.1039/d3dd00227fopenalex-snapshot
Pareto optimization to accelerate multi-objective virtual screening
inferred← citeshttps://doi.org/10.1080/07391102.2011.10507384openalex-snapshot
BetaDock: Shape-Priority Docking Method Based on Beta-Complex
inferred← citeshttps://doi.org/10.1080/07391102.2012.10507408openalex-snapshot
Computational Evidence to Inhibition of Human Acetyl Cholinesterase by Withanolide A for Alzheimer Treatment
inferred← citeshttps://doi.org/10.1080/07391102.2014.915764openalex-snapshot
Conserved residues at the MAPKs binding interfaces that regulate transcriptional machinery
inferred← citeshttps://doi.org/10.1080/07391102.2020.1823882openalex-snapshot
Computational simulation studies on the binding selectivity of Wee1 and Checkpoint kinase 1 by molecular dynamics simulation combined with free energy calculations
inferred← citeshttps://doi.org/10.1080/1062936x.2024.2306336openalex-snapshot
Docking and other computing tools in drug design against SARS-CoV-2
inferred← citeshttps://doi.org/10.1080/17460441.2025.2458666openalex-snapshot
Virtual screening: hope, hype, and the fine line in between
inferred← citeshttps://doi.org/10.1093/bib/bbx030openalex-snapshot
Comprehensive assessment of flexible-ligand docking algorithms: current effectiveness and challenges
inferred← citeshttps://doi.org/10.1093/nar/gkm1178openalex-snapshot
Identification and characterization of coumestans as novel HCV NS5B polymerase inhibitors
inferred← citeshttps://doi.org/10.1101/2023.11.23.568394openalex-snapshot
RNAmigos2: Fast and accurate structure-based RNA virtual screening with semi-supervised graph learning and large-scale docking data
inferred← citeshttps://doi.org/10.1101/2024.12.15.628585openalex-snapshot
EnzymeCAGE: A Geometric Foundation Model for Enzyme Retrieval with Evolutionary Insights
inferred← citeshttps://doi.org/10.1109/tcbb.2015.2415771openalex-snapshot
In-silico Studies Show Potent Inhibition of HIV-1 Reverse Transcriptase Activity by a Herbal Drug
inferred← citeshttps://doi.org/10.1111/bph.12233openalex-snapshot
Molecular modelling, synthesis, cytotoxicity and anti‐tumour mechanisms of 2‐aryl‐6‐substituted quinazolinones as dual‐targeted anti‐cancer agents
inferred← citeshttps://doi.org/10.1111/cbdd.12397openalex-snapshot
Molecular Modeling, Synthesis and Biological Evaluation of N‐Heteroaryl Compounds as Reverse Transcriptase Inhibitors Against HIV ‐1
inferred← citeshttps://doi.org/10.1111/cbdd.12470openalex-snapshot
TS ‐Chemscore, a Target‐Specific Scoring Function, Significantly Improves the Performance of Scoring in Virtual Screening
inferred← citeshttps://doi.org/10.1111/cbdd.13418openalex-snapshot
Structure‐based pharmacophore models to probe anticancer activity of inhibitors of protein kinase B‐beta (PKB β)
inferred← citeshttps://doi.org/10.1111/j.1476-5381.2010.00700.xopenalex-snapshot
Biochemical and molecular analysis of carboxylesterase‐mediated hydrolysis of cocaine and heroin
inferred← citeshttps://doi.org/10.1111/j.1747-0285.2010.00986.xopenalex-snapshot
Targeting the Dimerization of Epidermal Growth Factor Receptors with Small‐Molecule Inhibitors
inferred← citeshttps://doi.org/10.1111/j.1747-0285.2012.01430.xopenalex-snapshot
Design, Synthesis, Antibacterial Activity, and Molecular Docking Studies of Novel Hybrid 1,3‐Thiazine‐1,3,5‐Triazine Derivatives as Potential Bacterial Translation Inhibitor
inferred← citeshttps://doi.org/10.1124/mol.116.103432openalex-snapshot
Dipicrylamine Modulates GABAρ1 Receptors through Interactions with Residues in the TM4 and Cys-Loop Domains
inferred← citeshttps://doi.org/10.1142/9789814271820_0008openalex-snapshot
A STUDY OF HYDROPHOBIC EFFECT ON THE PROTEIN FOLDING USING MONTE CARLO
inferred← citeshttps://doi.org/10.1146/annurev.biophys.36.040306.132550openalex-snapshot
Calculation of Protein-Ligand Binding Affinities
inferred← citeshttps://doi.org/10.1155/2013/236850openalex-snapshot
Exploring Different Virtual Screening Strategies for Acetylcholinesterase Inhibitors
inferred← citeshttps://doi.org/10.11606/t.76.2015.tde-02102015-093453openalex-snapshot
Estudos estruturais e de química medicinal aplicados às enzimas da via glicolítica de protozoários: enolase de Plasmodium falciparum e gliceraldeído-3-fosfato desidrogenase de Trypanosoma cruzi
inferred← citeshttps://doi.org/10.1186/1471-2105-10-225openalex-snapshot
A statistical framework to evaluate virtual screening
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/s13321-015-0096-0openalex-snapshot
Modeling enzyme-ligand binding in drug discovery
inferred← citeshttps://doi.org/10.1186/s13321-016-0112-zopenalex-snapshot
vSDC: a method to improve early recognition in virtual screening when limited experimental resources are available
inferred← citeshttps://doi.org/10.1186/s13321-017-0227-xopenalex-snapshot
Efficient conformational sampling and weak scoring in docking programs? Strategy of the wisdom of crowds
inferred← citeshttps://doi.org/10.1186/s13321-025-01107-zopenalex-snapshot
Efficient decoy selection to improve virtual screening using machine learning models
inferred← citeshttps://doi.org/10.1186/s42238-025-00363-yopenalex-snapshot
In silico receptor binding and ex vivo nasal epithelial membrane permeation studies of selected phytocannabinoids
inferred← citeshttps://doi.org/10.13160/ricns.2013.6.2.100openalex-snapshot
Application of Docking Methods: An Effective In Silico Tool for Drug Design
inferred← citeshttps://doi.org/10.1360/n032015-00115openalex-snapshot
Development of a high-quality benchmark for scoring function assessment
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1000405openalex-snapshot
FINDSITELHM: A Threading-Based Approach to Ligand Homology Modeling
inferred← citeshttps://doi.org/10.1371/journal.pone.0168806openalex-snapshot
A 2D-QSAR and Grid-Independent Molecular Descriptor (GRIND) Analysis of Quinoline-Type Inhibitors of Akt2: Exploration of the Binding Mode in the Pleckstrin Homology (PH) Domain
inferred← citeshttps://doi.org/10.17192/z2007.0753openalex-snapshot
Leitstrukturoptimierung für Antiprotozoika und Erfolgreiche Leitstruktursuche für Metalloproteinasen: Ein Fragment-basiertes Virtuelles Screening Verfahren
inferred← citeshttps://doi.org/10.18632/oncotarget.834openalex-snapshot
Luteolin is a novel p90 ribosomal S6 kinase (RSK) inhibitor that suppresses Notch4 signaling by blocking the activation of Y-box binding protein-1 (YB-1)
inferred← citeshttps://doi.org/10.21007/etd.cghs.2008.0136openalex-snapshot
Structure- and Ligand-Based Design of Novel Antimicrobial Agents
inferred← citeshttps://doi.org/10.21203/rs.3.rs-3341477/v1openalex-snapshot
Ligand Based Pharmacophore Modeling, Virtual Screening, Molecular Docking, Molecular Dynamic simulation and In-silico ADMET Studies for the Discovery of Potential BACE-1 Inhibitors
inferred← citeshttps://doi.org/10.2174/0929867327666200504082256openalex-snapshot
In Silico Modelling in the Development of Novel Radiolabelled Peptide Probes
inferred← citeshttps://doi.org/10.2174/1381612811319120005openalex-snapshot
Scoring Functions for Prediction of Protein-Ligand Interactions
inferred← citeshttps://doi.org/10.2174/138620708784534761openalex-snapshot
G Protein β γ Subunits as Targets for Small Molecule Therapeutic Development
inferred← citeshttps://doi.org/10.2174/1570180819666220922103109openalex-snapshot
Molecular Docking: Principles, Advances, and Its Applications in Drug Discovery
inferred← citeshttps://doi.org/10.2174/1570180820666230725110021openalex-snapshot
In vitro Antibacterial Activity of Dye Compounds
inferred← citeshttps://doi.org/10.2174/1570180820666230731144315openalex-snapshot
In vitro and In silico Antibacterial Evaluation of N-Methyl-2-phenylmaleimides
inferred← citeshttps://doi.org/10.2174/157340909787580854openalex-snapshot
Combined Virtual Screening Strategies
inferred← citeshttps://doi.org/10.2174/157340909787580863openalex-snapshot
Computational Intelligence Methods for Docking Scores
inferred← citeshttps://doi.org/10.22159/ijpps.2021v13i8.41956openalex-snapshot
DATABASE ENRICHMENTS OF MAO-B THROUGH ENSEMBLE DOCKING
inferred← citeshttps://doi.org/10.2741/2974openalex-snapshot
4-Thiazolidinones: a novel class of hepatitis C virus NS5B polymerase inhibitors
inferred← citeshttps://doi.org/10.3109/14756366.2013.833196openalex-snapshot
PLS and shape-based similarity analysis of maleimides – GSK-3 inhibitors
inferred← citeshttps://doi.org/10.32657/10220/48075openalex-snapshot
Progesterone receptor ligand binding domain : from conformational dynamics to drug discovery
inferred← citeshttps://doi.org/10.33263/briac124.55915600openalex-snapshot
Molecular Docking and Molecular Dynamics Studies of SARS-CoV-2 Inhibitors: Crocin, Digitoxigenin, Beta-Eudesmol and Favipiravir: Comparative Study
inferred← citeshttps://doi.org/10.3389/fchem.2020.00167openalex-snapshot
Integrating Ligand and Target-Driven Based Virtual Screening Approaches With in vitro Human Cell Line Models and Time-Resolved Fluorescence Resonance Energy Transfer Assay to Identify Novel Hit Compounds Against BCL-2
inferred← citeshttps://doi.org/10.3389/fphar.2018.00260openalex-snapshot
Improving Docking Performance Using Negative Image-Based Rescoring
inferred← citeshttps://doi.org/10.3389/fphar.2022.1026306openalex-snapshot
Discovery of novel anti-tumor compounds targeting PARP-1 with induction of autophagy through in silico and in vitro screening
inferred← citeshttps://doi.org/10.3390/ijms11083016openalex-snapshot
Advances and Challenges in Protein-Ligand Docking
showing the first 200 of 219 · page through all 219
Editorial review for independent work. ICSAC — the Institute for Complexity
Science and Advanced Computing — runs a structured editorial panel for researchers
publishing outside journals, and publishes on CiteStamp rails. Submission is free
and goes through ORCID: icsacinstitute.org/submit.