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Outstanding challenges in protein–ligand docking and structure‐based virtual screening

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Outgoing claims: the papers this work cites, builds on, or argues with.

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The particle concept: placing discrete water molecules during protein-ligand docking predictions

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Evaluation of the FLEXX incremental construction algorithm for protein-ligand docking

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Application and Limitations of X‐ray Crystallographic Data in Structure‐Based Ligand and Drug Design

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Structure‐Based Optimization of Aldose Reductase Inhibitors Originating from Virtual Screening

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AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

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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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In Pursuit of Fully Flexible Protein‐Ligand Docking: Modeling the Bilateral Mechanism of Binding

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High‐energy water sites determine peptide binding affinity and specificity of PDZ domains

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Automated docking to multiple target structures: Incorporation of protein mobility and structural water heterogeneity in AutoDock

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Kinase inhibitors and the case for CH…O hydrogen bonds in protein–ligand binding

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Structure‐based identification of binding sites, native ligands and potential inhibitors for G‐protein coupled receptors

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Recovering the true targets of specific ligands by virtual screening of the protein data bank

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Virtual screening for inhibitors of human aldose reductase

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Comparing protein–ligand docking programs is difficult

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Minimizing false positives in kinase virtual screens

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FURSMASA: A new approach to rapid scoring functions that uses a MD‐averaged potential energy grid and a solvent‐accessible surface area term with parameters GA fit to experimental data

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A Fast Flexible Docking Method using an Incremental Construction Algorithm

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Predicting conserved water-mediated and polar ligand interactions in proteins using a K-nearest-neighbors genetic 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

inferredcites →https://doi.org/10.1006/jmbi.2001.4551openalex-snapshot

FlexE: efficient molecular docking considering protein structure variations

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FLOG: A system to select ?quasi-flexible? ligands complementary to a receptor of known three-dimensional structure

inferredcites →https://doi.org/10.1007/bf00126743openalex-snapshot

The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure

inferredcites →https://doi.org/10.1007/s00894-003-0129-xopenalex-snapshot

WaterScore: a novel method for distinguishing between bound and displaceable water molecules in the crystal structure of the binding site of protein-ligand complexes

inferredcites →https://doi.org/10.1007/s00894-008-0390-0openalex-snapshot

How sophisticated should a scoring function be to ensure successful docking, scoring and virtual screening?

inferredcites →https://doi.org/10.1007/s10822-006-9060-4openalex-snapshot

Development and validation of a modular, extensible docking program: DOCK 5

inferredcites →https://doi.org/10.1007/s10822-006-9065-zopenalex-snapshot

Modeling and active site refinement for G protein-coupled receptors: application to the β-2 adrenergic receptor

inferredcites →https://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?

inferredcites →https://doi.org/10.1007/s10822-007-9166-3openalex-snapshot

How to do an evaluation: pitfalls and traps

inferredcites →https://doi.org/10.1007/s10822-008-9170-2openalex-snapshot

What do we know and when do we know it?

inferredcites →https://doi.org/10.1007/s10822-008-9174-yopenalex-snapshot

Customizing scoring functions for docking

inferredcites →https://doi.org/10.1007/s10822-008-9181-zopenalex-snapshot

Managing bias in ROC curves

inferredcites →https://doi.org/10.1007/s10822-008-9188-5openalex-snapshot

A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE)

inferredcites →https://doi.org/10.1007/s10822-008-9189-4openalex-snapshot

Community benchmarks for virtual screening

inferredcites →https://doi.org/10.1007/s10822-008-9196-5openalex-snapshot

Recommendations for evaluation of computational methods

inferredcites →https://doi.org/10.1007/s10822-009-9276-1openalex-snapshot

Robust optimization of scoring functions for a target class

inferredcites →https://doi.org/10.1007/s10822-009-9303-2openalex-snapshot

Let’s not forget tautomers

inferredcites →https://doi.org/10.1016/0022-2836(91)90859-5openalex-snapshot

“Soft docking”: Matching of molecular surface cubes

inferredcites →https://doi.org/10.1016/j.bcp.2009.02.012openalex-snapshot

X-ray structure breakthroughs in the GPCR transmembrane region

inferredcites →https://doi.org/10.1016/j.bmc.2005.12.032openalex-snapshot

New insights about HERG blockade obtained from protein modeling, potential energy mapping, and docking studies

inferredcites →https://doi.org/10.1016/j.bmcl.2008.01.063openalex-snapshot

Use of the X-ray structure of the Beta2-adrenergic receptor for drug discovery

inferredcites →https://doi.org/10.1016/j.bmcl.2008.09.046openalex-snapshot

Use of the X-ray structure of the β2-adrenergic receptor for drug discovery. Part 2: Identification of active compounds

inferredcites →https://doi.org/10.1016/j.drudis.2006.05.012openalex-snapshot

Virtual ligand screening: strategies, perspectives and limitations

inferredcites →https://doi.org/10.1016/j.drudis.2007.05.004openalex-snapshot

Water, water everywhere — except where it matters?

inferredcites →https://doi.org/10.1016/j.drudis.2007.12.002openalex-snapshot

Towards improving compound selection in structure-based virtual screening

inferredcites →https://doi.org/10.1016/j.drudis.2008.06.006openalex-snapshot

Limitations and lessons in the use of X-ray structural information in drug design

inferredcites →https://doi.org/10.1016/j.jmb.2004.01.003openalex-snapshot

Protein Flexibility in Ligand Docking and Virtual Screening to Protein Kinases

inferredcites →https://doi.org/10.1016/j.jmgm.2008.09.002openalex-snapshot

Induced-fit docking of mometasone furoate and further evidence for glucocorticoid receptor 17α pocket flexibility

inferredcites →https://doi.org/10.1016/j.sbi.2008.01.004openalex-snapshot

Flexible ligand docking to multiple receptor conformations: a practical alternative

inferredcites →https://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”

inferredcites →https://doi.org/10.1016/s0006-3495(03)75033-4openalex-snapshot

Ligand-Induced Conformational Changes: Improved Predictions of Ligand Binding Conformations and Affinities

inferredcites →https://doi.org/10.1016/s0022-2836(05)80038-5openalex-snapshot

Ligand docking to proteins with discrete side-chain flexibility

inferredcites →https://doi.org/10.1016/s0022-2836(95)80037-9openalex-snapshot

Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation

inferredcites →https://doi.org/10.1016/s0169-409x(02)00003-0openalex-snapshot

Prediction of ‘drug-likeness’

inferredcites →https://doi.org/10.1016/s1093-3263(02)00164-xopenalex-snapshot

LigandFit: a novel method for the shape-directed rapid docking of ligands to protein active sites

inferredcites →https://doi.org/10.1016/s1093-3263(03)00123-2openalex-snapshot

Analysis and optimization of structure-based virtual screening protocols (1): exploration of ligand conformational sampling techniques

inferredcites →https://doi.org/10.1016/s1359-6446(04)03071-5openalex-snapshot

Computational Medicinal Chemistry for Drug Discovery

inferredcites →https://doi.org/10.1021/bi981848ropenalex-snapshot

Structure-Based Design of Potent Inhibitors of Scytalone Dehydratase: Displacement of a Water Molecule from the Active Site

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/ci0497861openalex-snapshot

Application of Machine Learning To Improve the Results of High-Throughput Docking Against the HIV-1 Protease

inferredcites →https://doi.org/10.1021/ci050185zopenalex-snapshot

Considerations in Compound Database Preparation“Hidden” Impact on Virtual Screening Results

inferredcites →https://doi.org/10.1021/ci0502855openalex-snapshot

Physics-Based Scoring of Protein−Ligand Complexes: Enrichment of Known Inhibitors in Large-Scale Virtual Screening

inferredcites →https://doi.org/10.1021/ci050407topenalex-snapshot

Ligand Bias of Scoring Functions in Structure-Based Virtual Screening

inferredcites →https://doi.org/10.1021/ci6002637openalex-snapshot

Docking Ligands into Flexible and Solvated Macromolecules. 1. Development and Validation of FITTED 1.0

inferredcites →https://doi.org/10.1021/ci6003527openalex-snapshot

Analysis of Ligand-Bound Water Molecules in High-Resolution Crystal Structures 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/ci6005036openalex-snapshot

Pose Prediction Accuracy in Docking Studies and Enrichment of Actives in the Active Site of GSK-3β

inferredcites →https://doi.org/10.1021/ci6005596openalex-snapshot

A Multivariate Approach to Investigate Docking Parameters' Effects on Docking Performance

inferredcites →https://doi.org/10.1021/ci700041jopenalex-snapshot

Rapid Estimation of Relative Protein−Ligand Binding Affinities Using a High-Throughput Version of MM-PBSA

inferredcites →https://doi.org/10.1021/ci700052xopenalex-snapshot

Comparison of Topological, Shape, and Docking Methods in Virtual Screening

inferredcites →https://doi.org/10.1021/ci700223popenalex-snapshot

Impact of Ligand Protonation on Virtual Screening against β-Secretase (BACE1)

inferredcites →https://doi.org/10.1021/ci700285eopenalex-snapshot

Ligand−Protein Docking with Water Molecules

inferredcites →https://doi.org/10.1021/ci700358ropenalex-snapshot

Computational Validation of the Importance of Absolute Stereochemistry in Virtual Screening

inferredcites →https://doi.org/10.1021/ci700470copenalex-snapshot

Investigation of MM-PBSA Rescoring of Docking Poses

inferredcites →https://doi.org/10.1021/ci800004wopenalex-snapshot

MM-GB/SA Rescoring of Docking Poses in Structure-Based Lead Optimization

inferredcites →https://doi.org/10.1021/ci8001167openalex-snapshot

MedusaScore: An Accurate Force Field-Based Scoring Function for Virtual Drug Screening

inferredcites →https://doi.org/10.1021/ci8002254openalex-snapshot

Protein−Ligand Docking against Non-Native Protein Conformers

inferredcites →https://doi.org/10.1021/ci800340jopenalex-snapshot

Tautomer Enumeration and Stability Prediction for Virtual Screening on Large Chemical Databases

inferredcites →https://doi.org/10.1021/ci800420zopenalex-snapshot

Influence of Protonation, Tautomeric, and Stereoisomeric States on Protein−Ligand Docking Results

inferredcites →https://doi.org/10.1021/ci8004308openalex-snapshot

Docking Ligands into Flexible and Solvated Macromolecules. 4. Are Popular Scoring Functions Accurate for this Class of Proteins?

inferredcites →https://doi.org/10.1021/ci800466nopenalex-snapshot

Position Specific Interaction Dependent Scoring Technique for Virtual Screening Based on Weighted Protein−Ligand Interaction Fingerprint Profiles

inferredcites →https://doi.org/10.1021/ci9000053openalex-snapshot

Comparative Assessment of Scoring Functions on a Diverse Test Set

inferredcites →https://doi.org/10.1021/ci900043ropenalex-snapshot

APIF: A New Interaction Fingerprint Based on Atom Pairs and Its Application to Virtual Screening

inferredcites →https://doi.org/10.1021/ci9000629openalex-snapshot

Effect of Input Differences on the Results of Docking Calculations

inferredcites →https://doi.org/10.1021/ci900068kopenalex-snapshot

Discovery of Wild-Type and Y181C Mutant Non-nucleoside HIV-1 Reverse Transcriptase Inhibitors Using Virtual Screening with Multiple Protein Structures

inferredcites →https://doi.org/10.1021/ci9001074openalex-snapshot

GARD: A Generally Applicable Replacement for RMSD

inferredcites →https://doi.org/10.1021/ci900164fopenalex-snapshot

Testing Assumptions and Hypotheses for Rescoring Success in Protein−Ligand Docking

inferredcites →https://doi.org/10.1021/ci900293eopenalex-snapshot

Role of Water in Molecular Docking Simulations of Cytochrome P450 2D6

inferredcites →https://doi.org/10.1021/ci9002987openalex-snapshot

Inclusion of Solvation and Entropy in the Knowledge-Based Scoring Function for Protein−Ligand Interactions

inferredcites →https://doi.org/10.1021/ci900364wopenalex-snapshot

The Effect of Ligand-Based Tautomer and Protomer Prediction on Structure-Based Virtual Screening

inferredcites →https://doi.org/10.1021/ci9003943openalex-snapshot

Recipes for the Selection of Experimental Protein Conformations for Virtual Screening

inferredcites →https://doi.org/10.1021/cr00023a012openalex-snapshot

From atoms and bonds to three-dimensional atomic coordinates: automatic model builders

inferredcites →https://doi.org/10.1021/ct100102qopenalex-snapshot

Limits of Free Energy Computation for Protein−Ligand Interactions

inferredcites →https://doi.org/10.1021/ja0524604openalex-snapshot

Thermal Equilibrium of High- and Low-Spin Forms of Cytochrome P450 BM-3: Repositioning of the Substrate?

inferredcites →https://doi.org/10.1021/jm020406hopenalex-snapshot

Surflex: Fully Automatic Flexible Molecular Docking Using a Molecular Similarity-Based Search Engine

inferredcites →https://doi.org/10.1021/jm030331xopenalex-snapshot

Structural Interaction Fingerprint (SIFt): A Novel Method for Analyzing Three-Dimensional Protein−Ligand Binding Interactions

inferredcites →https://doi.org/10.1021/jm030363kopenalex-snapshot

Finding More Needles in the Haystack: A Simple and Efficient Method for Improving High-Throughput Docking Results

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/jm048972vopenalex-snapshot

Unveiling the Full Potential of Flexible Receptor Docking Using Multiple Crystallographic Structures

inferredcites →https://doi.org/10.1021/jm0493360openalex-snapshot

PostDOCK: A Structural, Empirical Approach to Scoring Protein Ligand Complexes

inferredcites →https://doi.org/10.1021/jm049756popenalex-snapshot

Soft Docking and Multiple Receptor Conformations in Virtual Screening

inferredcites →https://doi.org/10.1021/jm049970dopenalex-snapshot

Combination of a Naive Bayes Classifier with Consensus Scoring Improves Enrichment of High-Throughput Docking Results

inferredcites →https://doi.org/10.1021/jm050196jopenalex-snapshot

Receptor Flexibility in de Novo Ligand Design and Docking

inferredcites →https://doi.org/10.1021/jm0503594openalex-snapshot

5-Cyanopyrimidine Derivatives as a Novel Class of Potent, Selective, and Orally Active Inhibitors of p38α MAP Kinase

inferredcites →https://doi.org/10.1021/jm050362nopenalex-snapshot

A Critical Assessment of Docking Programs and Scoring Functions

inferredcites →https://doi.org/10.1021/jm050540copenalex-snapshot

Novel Procedure for Modeling Ligand/Receptor Induced Fit Effects

inferredcites →https://doi.org/10.1021/jm050543popenalex-snapshot

Modeling Water Molecules in Protein−Ligand Docking Using GOLD

inferredcites →https://doi.org/10.1021/jm051256oopenalex-snapshot

Extra Precision Glide: Docking and Scoring Incorporating a Model of Hydrophobic Enclosure for Protein−Ligand Complexes

inferredcites →https://doi.org/10.1021/jm060167oopenalex-snapshot

Do Structurally Similar Ligands Bind in a Similar Fashion?

inferredcites →https://doi.org/10.1021/jm0603365openalex-snapshot

Comparison of Shape-Matching and Docking as Virtual Screening Tools

inferredcites →https://doi.org/10.1021/jm060522aopenalex-snapshot

Accurate Prediction of the Relative Potencies of Members of a Series of Kinase Inhibitors Using Molecular Docking and MM-GBSA Scoring

inferredcites →https://doi.org/10.1021/jm0608356openalex-snapshot

Benchmarking Sets for Molecular Docking

inferredcites →https://doi.org/10.1021/jm060999mopenalex-snapshot

Prediction of Protein−Ligand Interactions. Docking and Scoring: Successes and Gaps

inferredcites →https://doi.org/10.1021/jm061277yopenalex-snapshot

Diverse, High-Quality Test Set for the Validation of Protein−Ligand Docking Performance

inferredcites →https://doi.org/10.1021/jm100112jopenalex-snapshot

A Medicinal Chemist’s Guide to Molecular Interactions

inferredcites →https://doi.org/10.1021/jm701023hopenalex-snapshot

Robust Classification of “Relevant” Water Molecules in Putative Protein Binding Sites

inferredcites →https://doi.org/10.1021/jm701248topenalex-snapshot

Docking Study Yields Four Novel Inhibitors of the Protooncogene Pim-1 Kinase

inferredcites →https://doi.org/10.1021/jm701255bopenalex-snapshot

Ligand Binding Efficiency: Trends, Physical Basis, and Implications

inferredcites →https://doi.org/10.1021/jm800217kopenalex-snapshot

Flexible Side Chain Models Improve Enrichment Rates in In Silico Screening

inferredcites →https://doi.org/10.1021/jm800562dopenalex-snapshot

Target Flexibility: An Emerging Consideration in Drug Discovery and Design

inferredcites →https://doi.org/10.1021/jm8006239openalex-snapshot

Exploiting Ordered Waters in Molecular Docking

inferredcites →https://doi.org/10.1021/jm801444xopenalex-snapshot

Large-Scale Application of High-Throughput Molecular Mechanics with Poisson−Boltzmann Surface Area for Routine Physics-Based Scoring of Protein−Ligand Complexes

inferredcites →https://doi.org/10.1021/jm8016464openalex-snapshot

Structural Artifacts in Protein−Ligand X-ray Structures: Implications for the Development of Docking Scoring Functions

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/10.1021/jm990352kopenalex-snapshot

Consensus Scoring: A Method for Obtaining Improved Hit Rates from Docking Databases of Three-Dimensional Structures into Proteins

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/a:1011115820450openalex-snapshot

DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases

inferredcites →https://doi.org/10.1038/381272a0openalex-snapshot

Errors in protein structures

inferredcites →https://doi.org/10.1038/nrd3139openalex-snapshot

Virtual screening: an endless staircase?

inferredcites →https://doi.org/10.1038/nsmb0306-184openalex-snapshot

Is one solution good enough?

inferredcites →https://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

inferredcites →https://doi.org/10.1039/9781847557964openalex-snapshot

Computational and Structural Approaches to Drug Discovery

inferredcites →https://doi.org/10.1073/pnas.0812657106openalex-snapshot

Structure-based discovery of β 2 -adrenergic receptor ligands

inferredcites →https://doi.org/10.1074/jbc.m512688200openalex-snapshot

Structural and Molecular Interactions of CCR5 Inhibitors with CCR5

inferredcites →https://doi.org/10.1074/jbc.m802200200openalex-snapshot

(-)-Epigallocatechin Gallate Regulates CD3-mediated T Cell Receptor Signaling in Leukemia through the Inhibition of ZAP-70 Kinase

inferredcites →https://doi.org/10.1110/ps.041153605openalex-snapshot

Side‐chain flexibility in protein–ligand binding: The minimal rotation hypothesis

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Novel PPAR‐gamma Agonists Identified from a Natural Product Library: A Virtual Screening, Induced‐Fit Docking and Biological Assay Study

inferredcites →https://doi.org/10.1126/science.8278812openalex-snapshot

Rational Design of Potent, Bioavailable, Nonpeptide Cyclic Ureas as HIV Protease Inhibitors

inferredcites →https://doi.org/10.1158/0008-5472.can-08-4959openalex-snapshot

A Regulatory Mechanism for RSK2 NH2-Terminal Kinase Activity

inferredcites →https://doi.org/10.1186/1758-2946-2-s1-p25openalex-snapshot

Ensemble docking revisited

inferredcites →https://doi.org/10.1201/9781420028775openalex-snapshot

Virtual Screening in Drug Discovery

inferredcites →https://doi.org/10.1385/1-59259-964-8:375openalex-snapshot

Chemical Database Preparation for Compound Acquisition or Virtual Screening

inferredcites →https://doi.org/10.1517/17460441.1.4.335openalex-snapshot

Incorporating protein flexibility into docking and structure-based drug design

inferredcites →https://doi.org/10.2174/092986706778521797openalex-snapshot

Docking and Scoring - Theoretically Easy, Practically Impossible?

inferredcites →https://doi.org/10.2174/092986708783330566openalex-snapshot

Theoretical and Practical Considerations in Virtual Screening: A Beaten Field?

inferredcites →https://doi.org/10.2174/092986709789057680openalex-snapshot

Conformational Sampling and Energetics of Drug-Like Molecules

inferredcites →https://doi.org/10.2174/138620709787581666openalex-snapshot

Docking-Based Virtual Screening: Recent Developments

inferredcites →https://doi.org/10.2174/138620709788167980openalex-snapshot

Machine Learning in Virtual Screening

inferredcites →https://doi.org/10.2174/138620709788489046openalex-snapshot

Bayesian Modeling in Virtual High Throughput Screening

inferredcites →https://doi.org/10.2174/138620709789824682openalex-snapshot

Structure-Based Virtual Ligand Screening: Recent Success Stories

inferredcites →https://doi.org/10.2174/138920306778559395openalex-snapshot

Scoring Functions for Protein-Ligand Docking

inferredcites →https://doi.org/10.2174/138955708783331540openalex-snapshot

Essential Factors for Successful Virtual Screening

inferredcites →https://doi.org/10.2174/156802607780906753openalex-snapshot

Ligand Docking and Structure-based Virtual Screening in Drug Discovery

inferredcites →https://doi.org/10.2174/156802607781696846openalex-snapshot

The Role of Halogen Bonding in Inhibitor Recognition and Binding by Protein Kinases

inferredcites →https://doi.org/10.2174/156802609789207091openalex-snapshot

Docking Screens: Right for the Right Reasons?

inferredcites →https://doi.org/10.2174/156802609789207127openalex-snapshot

Structure-Based Drug Design Strategies in Medicinal Chemistry

inferredcites →https://doi.org/10.2174/157340607779317481openalex-snapshot

Processing of Small Molecule Databases for Automated Docking

inferredcites →https://doi.org/10.2174/157340905774330291openalex-snapshot

The Challenge of Considering Receptor Flexibility in Ligand Docking and Virtual Screening

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Virtual Docking: How Are We Doing And How Can We Improve?

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Protein–Ligand Interactions: Computational Docking

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Virtual Screening: AnIn SilicoApproach to Flavor Compounds

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The statistical significance of selected sense–antisense peptide interactions

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Latest developments in molecular docking: 2010–2011 in review

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Using the Semiempirical Quantum Mechanics in Improving the Molecular Docking: A Case Study with CDK2

inferred← citeshttps://doi.org/10.1002/minf.202200135openalex-snapshot

GB‐score: Minimally designed machine learning scoring function based on distance‐weighted interatomic contact features

inferred← citeshttps://doi.org/10.1002/prot.24104openalex-snapshot

PRL‐dock: Protein‐ligand docking based on hydrogen bond matching and probabilistic relaxation labeling

inferred← citeshttps://doi.org/10.1002/prot.24210openalex-snapshot

Solvated protein–protein docking using Kyte‐Doolittle‐based water preferences

inferred← citeshttps://doi.org/10.1002/prot.24410openalex-snapshot

Applying conformational selection theory to improve crossdocking efficiency in 3‐phosphoinositide dependent protein kinase‐1

inferred← citeshttps://doi.org/10.1002/qua.25678openalex-snapshot

Computational chemistry in drug lead discovery and design

inferred← citeshttps://doi.org/10.1002/slct.202500093openalex-snapshot

In Silico Evaluation of Approved Drug Library to Discover Tyrosine Threonine Kinase Inhibitors for Colon Cancer

inferred← citeshttps://doi.org/10.1002/slct.202502490openalex-snapshot

Mechanistic Insights into the Antispasmodic and Anti‐Inflammatory Activities of Dysphania ambrosioides L. Hydroethanolic Extract: A Combined In Vitro, In Vivo, and In Silico Approach

inferred← citeshttps://doi.org/10.1002/wcms.1225openalex-snapshot

Machine‐learning scoring functions to improve structure‐based binding affinity prediction and virtual screening

inferred← citeshttps://doi.org/10.1002/wcms.1567openalex-snapshot

Featurization strategies for protein–ligand interactions and their applications in scoring function development

inferred← citeshttps://doi.org/10.1002/wcms.1571openalex-snapshot

RNA –ligand molecular docking: Advances and challenges

inferred← citeshttps://doi.org/10.1002/wcms.1585openalex-snapshot

Along the allostery stream: Recent advances in computational methods for allosteric drug discovery

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In Silico Screening of Compound Libraries Using a Consensus of Orthogonal Methodologies

inferred← citeshttps://doi.org/10.1007/978-1-62703-342-8_1openalex-snapshot

Virtual Screening in Drug Design

inferred← citeshttps://doi.org/10.1007/978-3-319-10226-9_1openalex-snapshot

Introduction to Molecular Similarity and Chemical Space

inferred← citeshttps://doi.org/10.1007/978-981-10-8064-7_7openalex-snapshot

Plant Metabolites as New Leads to Anticancer Drug Discovery: Approaches and Challenges

inferred← citeshttps://doi.org/10.1007/978-981-15-8127-4_19openalex-snapshot

Molecular Docking Studies of Plant-Derived Bioactive Compounds: A Comprehensive In Silico Standardization Approach

inferred← citeshttps://doi.org/10.1007/978-981-19-5399-6_8openalex-snapshot

Drug Repurposing in Cancer

inferred← citeshttps://doi.org/10.1007/978-981-96-3041-7_18openalex-snapshot

RNA–Ligand Molecular Docking

inferred← citeshttps://doi.org/10.1007/s00044-011-9941-5openalex-snapshot

In silico screening of indinavir-based compounds targeting proteolytic activity in HIV PR: binding pocket fit approach

inferred← citeshttps://doi.org/10.1007/s00044-014-0910-7openalex-snapshot

Integrating molecular docking, CoMFA analysis, and machine-learning classification with virtual screening toward identification of novel scaffolds as Plasmodium falciparum enoyl acyl carrier protein reductase inhibitor

inferred← citeshttps://doi.org/10.1007/s00044-018-2253-2openalex-snapshot

Synthesis, antitrypanosomal activity and molecular docking studies of pyrimidine derivatives

inferred← citeshttps://doi.org/10.1007/s00249-016-1188-0openalex-snapshot

Investigation of the binding mode of 1, 3, 4-oxadiazole derivatives as amide-based inhibitors for soluble epoxide hydrolase (sEH) by molecular docking and MM-GBSA

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/s10822-023-00543-zopenalex-snapshot

Binding of small molecule inhibitors to RNA polymerase-Spt5 complex impacts RNA and DNA stability

inferred← citeshttps://doi.org/10.1007/s11030-021-10243-1openalex-snapshot

A multi-conformational virtual screening approach based on machine learning targeting PI3Kγ

inferred← citeshttps://doi.org/10.1007/s12154-012-0072-3openalex-snapshot

3D-QSAR studies of triazolopyrimidine derivatives of Plasmodium falciparum dihydroorotate dehydrogenase inhibitors using a combination of molecular dynamics, docking, and genetic algorithm-based methods

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/10.1016/b978-0-12-802508-6.00027-2openalex-snapshot

Practical Considerations in Virtual Screening and Molecular Docking

inferred← citeshttps://doi.org/10.1016/b978-0-12-821972-0.00009-5openalex-snapshot

Advanced biotechnology-based therapeutics

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Recent advances in the discovery and development of protein- protein interaction modulators by virtual screening

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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.biotechadv.2015.08.001openalex-snapshot

Discovery and resupply of pharmacologically active plant-derived natural products: A review

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On scaffold hopping: Challenges in the discovery of sulfated small molecules as mimetics of glycosaminoglycans

inferred← citeshttps://doi.org/10.1016/j.camwa.2012.01.060openalex-snapshot

Data extraction module—A supplementary tool for the AMMOS_ProtLig software package

inferred← citeshttps://doi.org/10.1016/j.carres.2013.03.012openalex-snapshot

An in silico virtual screening study for the design of norovirus inhibitors: fragment-based molecular docking and binding free energy calculations

inferred← citeshttps://doi.org/10.1016/j.compbiomed.2023.107737openalex-snapshot

Integrating biocomputational techniques for Breast cancer drug discovery via the HER-2, BCRA, VEGF and ER protein targets

inferred← citeshttps://doi.org/10.1016/j.drudis.2013.02.004openalex-snapshot

Collaborative virtual organisation and infrastructure for drug discovery

inferred← citeshttps://doi.org/10.1016/j.drudis.2024.103985openalex-snapshot

The present state and challenges of active learning in drug discovery

inferred← citeshttps://doi.org/10.1016/j.jmgm.2012.12.001openalex-snapshot

Assessment of new anti-HER2 ligands using combined docking, QM/MM scoring and MD simulation

inferred← citeshttps://doi.org/10.1016/j.jmgm.2013.06.004openalex-snapshot

In silico design: Extended molecular dynamic simulations of a new series of dually acting inhibitors against EGFR and HER2

inferred← citeshttps://doi.org/10.1016/j.jmgm.2016.04.003openalex-snapshot

Determination of the protonation state for the catalytic dyad in β-secretase when bound to hydroxyethylamine transition state analogue inhibitors: A molecular dynamics simulation study

inferred← citeshttps://doi.org/10.1016/j.jmgm.2018.07.008openalex-snapshot

G-score: A function to solve the puzzle of modeling the protonation states of β-secretase binding pocket

inferred← citeshttps://doi.org/10.1016/j.jmgm.2023.108434openalex-snapshot

Application of computational methods for class A GPCR Ligand discovery

inferred← citeshttps://doi.org/10.1016/j.jmgm.2024.108746openalex-snapshot

Binding interactions and in silico ADME prediction of isoconessimine derivatives as potent acetylcholinesterase inhibitors

inferred← citeshttps://doi.org/10.1016/j.jpba.2019.112982openalex-snapshot

Pharmaceutical analysis combined with in-silico therapeutic and toxicological profiling on zileuton and its impurities to assist in modern drug discovery

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/10.1021/acs.accounts.6b00491openalex-snapshot

Forging the Basis for Developing Protein–Ligand Interaction Scoring Functions

inferred← citeshttps://doi.org/10.1021/acs.biochem.2c00649openalex-snapshot

Rosetta’s Predictive Ability for Low-Affinity Ligand Binding in Fragment-Based Drug Discovery

inferred← citeshttps://doi.org/10.1021/acs.jcim.5b00512openalex-snapshot

Knodle: A Support Vector Machines-Based Automatic Perception of Organic Molecules from 3D Coordinates

inferred← citeshttps://doi.org/10.1021/acs.jcim.6b00749openalex-snapshot

The Development of Target-Specific Pose Filter Ensembles To Boost Ligand Enrichment for Structure-Based Virtual Screening

inferred← citeshttps://doi.org/10.1021/acs.jcim.8b00004openalex-snapshot

Maximal Unbiased Benchmarking Data Sets for Human Chemokine Receptors and Comparative Analysis

inferred← citeshttps://doi.org/10.1021/acs.jmedchem.5b00886openalex-snapshot

OpenGrowth: An Automated and Rational Algorithm for Finding New Protein Ligands

inferred← citeshttps://doi.org/10.1021/acsomega.3c01907openalex-snapshot

Pharmacological Basis for Antispasmodic, Bronchodilator, and Antidiarrheal Potential of Dryopteris ramosa (Hope) C. via In Vitro, In Vivo, and In Silico Studies

inferred← citeshttps://doi.org/10.1021/ci200611topenalex-snapshot

Protonation States of the Catalytic Dyad of β-Secretase (BACE1) in the Presence of Chemically Diverse Inhibitors: A Molecular Docking Study

inferred← citeshttps://doi.org/10.1021/ci3005786openalex-snapshot

Hydration Properties of Ligands and Drugs in Protein Binding Sites: Tightly-Bound, Bridging Water Molecules and Their Effects and Consequences on Molecular Design Strategies

inferred← citeshttps://doi.org/10.1021/ci4000294openalex-snapshot

TRAPP: A Tool for Analysis ofTransient BindingPockets inProteins

inferred← citeshttps://doi.org/10.1021/ci400040dopenalex-snapshot

Docking Challenge: Protein Sampling and Molecular Docking Performance

inferred← citeshttps://doi.org/10.1038/s41598-021-04448-5openalex-snapshot

Ensemble learning from ensemble docking: revisiting the optimum ensemble size problem

inferred← citeshttps://doi.org/10.1039/c3cp53511hopenalex-snapshot

A steered molecular dynamics mediated hit discovery for histone deacetylases

inferred← citeshttps://doi.org/10.1039/c5cp01498kopenalex-snapshot

Optical properties of prodigiosin and obatoclax: action spectroscopy and theoretical calculations

inferred← citeshttps://doi.org/10.1039/c9cp06303jopenalex-snapshot

Combined strategies in structure-based virtual screening

inferred← citeshttps://doi.org/10.1039/d1sc06946bopenalex-snapshot

PIGNet: a physics-informed deep learning model toward generalized drug–target interaction predictions

inferred← citeshttps://doi.org/10.1080/07391102.2023.2276879openalex-snapshot

Exploring the potential of biologically active phenolic acids from marine natural products as anticancer agents targeting the epidermal growth factor receptor

inferred← citeshttps://doi.org/10.1080/08927014.2021.1876849openalex-snapshot

Databases for the study of biofilms: current status and potential applications

inferred← citeshttps://doi.org/10.1080/17460441.2023.2171984openalex-snapshot

Advances in the discovery of new chemotypes through ultra-large library docking

inferred← citeshttps://doi.org/10.1093/abbs/gmv100openalex-snapshot

Computational allosteric ligand binding site identification on Ras proteins

inferred← citeshttps://doi.org/10.1093/bib/bbac520openalex-snapshot

A fully differentiable ligand pose optimization framework guided by deep learning and a traditional scoring function

inferred← citeshttps://doi.org/10.1093/bib/bbac626openalex-snapshot

Reducing false positive rate of docking-based virtual screening by active learning

inferred← citeshttps://doi.org/10.1101/2022.12.20.521309openalex-snapshot

End-to-end protein-ligand complex structure generation with diffusion-based generative models

inferred← citeshttps://doi.org/10.1109/access.2020.3026479openalex-snapshot

Prediction of Drug-Target Interactions by Ensemble Learning Method From Protein Sequence and Drug Fingerprint

inferred← citeshttps://doi.org/10.1111/cbdd.13820openalex-snapshot

A unique ligand‐steered strategy for CC chemokine receptor 2 homology modeling to facilitate structure‐based virtual screening

inferred← citeshttps://doi.org/10.1142/s0219720022500238openalex-snapshot

GCMCDTI: Graph convolutional autoencoder framework for predicting drug–target interactions based on matrix completion

inferred← citeshttps://doi.org/10.1155/2018/3924608openalex-snapshot

Structure-Based Drug Design for Cytochrome P450 Family 1 Inhibitors

inferred← citeshttps://doi.org/10.1155/2018/6247306openalex-snapshot

Smilax aristolochiifolia Root Extract and Its Compounds Chlorogenic Acid and Astilbin Inhibit the Activity of α‐Amylase and α‐Glucosidase Enzymes

inferred← citeshttps://doi.org/10.11606/d.9.2021.tde-05082021-002930openalex-snapshot

Reposicionamento de fármacos para o tratamento da doença de Chagas: desenvolvimento de modelos computacionais baseados em ligantes ativos fenotipicamente contra o >i /i< e na inibição da diidroorotato desidrog

inferred← citeshttps://doi.org/10.11606/t.76.2013.tde-29052013-103008openalex-snapshot

Identificação de novos inibidores da enzima aldolase de Trypanosoma brucei

inferred← citeshttps://doi.org/10.1186/1472-6807-14-18openalex-snapshot

A simple method for finding a protein’s ligand-binding pockets

inferred← citeshttps://doi.org/10.1186/s12859-023-05354-5openalex-snapshot

End-to-end protein–ligand complex structure generation with diffusion-based generative models

inferred← citeshttps://doi.org/10.1186/s13020-023-00763-3openalex-snapshot

Expanding potential targets of herbal chemicals by node2vec based on herb–drug interactions

inferred← citeshttps://doi.org/10.1186/s13321-021-00549-5openalex-snapshot

Investigation of pharmacological mechanism of natural product using pathway fingerprints similarity based on “drug-target-pathway” heterogenous network

inferred← citeshttps://doi.org/10.1186/s13321-022-00661-0openalex-snapshot

Chemoinformatics and artificial intelligence colloquium: progress and challenges in developing bioactive compounds

inferred← citeshttps://doi.org/10.1371/journal.pcbi.1002397openalex-snapshot

AutoClickChem: Click Chemistry in Silico

inferred← citeshttps://doi.org/10.1371/journal.pcbi.1013030openalex-snapshot

Ten quick tips to perform meaningful and reproducible molecular docking calculations

inferred← citeshttps://doi.org/10.1371/journal.pone.0156543openalex-snapshot

A Large and Phylogenetically Diverse Class of Type 1 Opsins Lacking a Canonical Retinal Binding Site

inferred← citeshttps://doi.org/10.1515/zpch-2021-3119openalex-snapshot

Binding interaction of benzamide derivatives as inhibitors of DNA gyrase and Sec14p using Molegro Virtual Docker based on binding free energy

inferred← citeshttps://doi.org/10.18632/oncotarget.20915openalex-snapshot

Virtual screening approach to identifying influenza virus neuraminidase inhibitors using molecular docking combined with machine-learning-based scoring function

inferred← citeshttps://doi.org/10.2174/1386207322666190927143026openalex-snapshot

From the Explored to the Unexplored: Computer-Tailored Drug Design Attempts in the Discovery of Selective Caspase Inhibitors

inferred← citeshttps://doi.org/10.2174/1568026614666140929120749openalex-snapshot

Virtual Screening Strategies in Medicinal Chemistry: The State of the Art and Current Challenges

inferred← citeshttps://doi.org/10.2174/1568026619666181120142141openalex-snapshot

Application of Computational Techniques to Unravel Structure-Function Relationship and their Role in Therapeutic Development

inferred← citeshttps://doi.org/10.23917/pharmacon.v13i2.14openalex-snapshot

EXPLORING 3D MOLECULAR STUDIES OF DIKETOPIPERAZINE ANALOGUES ON Staphylococcus aureus DEHYDROSQUALENE SYNTHASE USING GLIDE-XP

inferred← citeshttps://doi.org/10.26434/chemrxiv-2022-nr0dmopenalex-snapshot

Chemoinformatics and Artificial Intelligence Colloquium: Progress and Challenges to Develop Bioactive Compounds

inferred← citeshttps://doi.org/10.32469/10355/90175openalex-snapshot

Theoretical and computational modeling of rna-ligand interactions

inferred← citeshttps://doi.org/10.3389/fphar.2018.01134openalex-snapshot

Network-Based Methods for Prediction of Drug-Target Interactions

inferred← citeshttps://doi.org/10.3390/antibiotics9080480openalex-snapshot

Plant-Based Phytochemicals as Possible Alternative to Antibiotics in Combating Bacterial Drug Resistance

inferred← citeshttps://doi.org/10.3390/ijms222011191openalex-snapshot

Screening of β1- and β2-Adrenergic Receptor Modulators through Advanced Pharmacoinformatics and Machine Learning Approaches

inferred← citeshttps://doi.org/10.3390/ijms25031798openalex-snapshot

Virtual Screening of Peptide Libraries: The Search for Peptide-Based Therapeutics Using Computational Tools

inferred← citeshttps://doi.org/10.3390/metabo13101104openalex-snapshot

An Integrated Molecular Networking and Docking Approach to Characterize the Metabolome of Helichrysum splendidum and Its Pharmaceutical Potentials

inferred← citeshttps://doi.org/10.3390/molecules20021872openalex-snapshot

Natural Products as Leads in Schistosome Drug Discovery

inferred← citeshttps://doi.org/10.3390/molecules26175359openalex-snapshot

Prediction of Drug–Target Interactions by Combining Dual-Tree Complex Wavelet Transform with Ensemble Learning Method

inferred← citeshttps://doi.org/10.3998/ark.5550190.p009.605openalex-snapshot

Synthesis of Nα-protected amino/peptide Weinreb amides employing N,N'-carbonyldiimidazole as activating agent; studies on docking and antibacterial activities

inferred← citeshttps://doi.org/10.48550/arxiv.1305.6666openalex-snapshot

In Silico Design, Extended Molecular Dynamic Simulations and Binding Energy Calculations for a New Series of Dually Acting Inhibitors against EGFR and HER2

inferred← citeshttps://doi.org/10.52586/s551openalex-snapshot

Approaches for network based drug discovery

inferred← citeshttps://doi.org/10.5772/intechopen.100665openalex-snapshot

Molecular Docking - Recent Advances

inferred← citeshttps://doi.org/10.5772/intechopen.105815openalex-snapshot

Fundamentals of Molecular Docking and Comparative Analysis of Protein–Small-Molecule Docking Approaches

inferred← citeshttps://doi.org/10.6084/m9.figshare.26593283openalex-snapshot

Additional file 1 of Expanding potential targets of herbal chemicals by node2vec based on herb–drug interactions

inferred← citeshttps://doi.org/10.6084/m9.figshare.26594075openalex-snapshot

Additional file 1 of End-to-end protein–ligand complex structure generation with diffusion-based generative models

inferred← citeshttps://doi.org/10.70675/f278a628z9cf1z4408za15fzfed05518864eopenalex-snapshot

Techniques computationnelles avancées pour aider la conception rationnelle de petites molécules ciblant l'ARN

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