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Beyond the Virtual Screening Paradigm: Structure-Based Searching for New Lead Compounds

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What this work says

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

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Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function

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

inferredcites →https://doi.org/10.1002/3527609164openalex-snapshot

Pharmacophores and Pharmacophore Searches

inferredcites →https://doi.org/10.1002/9783527619368openalex-snapshot

Bioinformatics‐From Genomes to Therapies

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A point‐charge force field for molecular mechanics simulations of proteins based on condensed‐phase quantum mechanical calculations

inferredcites →https://doi.org/10.1002/jcc.540130412openalex-snapshot

Automated docking with grid‐based energy evaluation

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/prot.10266openalex-snapshot

Pharmacophore‐based molecular docking to account for ligand flexibility

inferredcites →https://doi.org/10.1002/prot.20217openalex-snapshot

FlexX‐Scan: Fast, structure‐based virtual screening

inferredcites →https://doi.org/10.1002/prot.20897openalex-snapshot

On the nature of cavities on protein surfaces: Application to the identification of drug‐binding sites

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A Fast Flexible Docking Method using an Incremental Construction Algorithm

inferredcites →https://doi.org/10.1007/s10822-006-9087-6openalex-snapshot

PHASE: a new engine for pharmacophore perception, 3D QSAR model development, and 3D database screening: 1. Methodology and preliminary results

inferredcites →https://doi.org/10.1007/s10822-007-9103-5openalex-snapshot

TrixX: structure-based molecule indexing for large-scale virtual screening in sublinear time

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/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/s1359-6446(00)01516-6openalex-snapshot

The in silico world of virtual libraries

inferredcites →https://doi.org/10.1021/ci010366aopenalex-snapshot

Is There a Difference between Leads and Drugs? A Historical Perspective

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/ci049885eopenalex-snapshot

LigandScout: 3-D Pharmacophores Derived from Protein-Bound Ligands and Their Use as Virtual Screening Filters

inferredcites →https://doi.org/10.1021/ci700368popenalex-snapshot

Novel Approach to Structure-Based Pharmacophore Search Using Computational Geometry and Shape Matching Techniques

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/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/jm701255bopenalex-snapshot

Ligand Binding Efficiency: Trends, Physical Basis, and Implications

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

Target Flexibility: An Emerging Consideration in Drug Discovery and Design

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/10.1023/a:1016399411208openalex-snapshot

Flexible docking under pharmacophore type constraints

inferredcites →https://doi.org/10.1023/a:1021242018286openalex-snapshot

A validation study on the practical use of automated de novo design

inferredcites →https://doi.org/10.1038/nrd2220openalex-snapshot

A decade of fragment-based drug design: strategic advances and lessons learned

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/10.1177/1087057104271957openalex-snapshot

Evaluating Real-Life High-Throughput Screening Data

inferredcites →https://doi.org/10.1351/pac199870051129openalex-snapshot

Glossary of terms used in medicinal chemistry (IUPAC Recommendations 1998)

inferredcites →https://doi.org/10.2174/1381612033454595openalex-snapshot

Conformational Flexibility Models for the Receptor in Structure Based Drug Design

What points at this work

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

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Structure‐Based Virtual Screening

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In silico Design, Synthesis, and Screening of Novel Deoxyhypusine Synthase Inhibitors Targeting HIV‐1 Replication

inferred← citeshttps://doi.org/10.1002/jcc.23094openalex-snapshot

Fast force field‐based optimization of protein–ligand complexes with graphics processor

inferred← citeshttps://doi.org/10.1002/jmr.1077openalex-snapshot

Challenges and advances in computational docking: 2009 in review

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/10.1007/978-1-60761-839-3_11openalex-snapshot

Pharmacophore-Based Virtual Screening

inferred← citeshttps://doi.org/10.1007/978-1-60761-931-4_6openalex-snapshot

Application of QSAR and Shape Pharmacophore Modeling Approaches for Targeted Chemical Library Design

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Anti-inflammatory potential of the CISACN adduct in LPS-induced murine models

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An integrated approach to knowledge-driven structure-based virtual screening

inferred← citeshttps://doi.org/10.1007/s12551-013-0130-2openalex-snapshot

Receptor–ligand molecular docking

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Principles of computational drug designing and drug repurposing—An algorithmic approach

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From cheminformatics to structure-based design: Web services and desktop applications based on the NAOMI library

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Molecular docking in pesticide resistance research: Applications, advances, limitations, and experimental validation

inferred← citeshttps://doi.org/10.1021/acs.jcim.0c01095openalex-snapshot

A Consistent Scheme for Gradient-Based Optimization of Protein – Ligand Poses

inferred← citeshttps://doi.org/10.1021/acs.jcim.3c01573openalex-snapshot

Redocking the PDB

inferred← citeshttps://doi.org/10.1021/ci300469hopenalex-snapshot

Fast Protein Binding Site Comparison via an Index-Based Screening Technology

inferred← citeshttps://doi.org/10.1021/ci500130eopenalex-snapshot

Facing the Challenges of Structure-Based Target Prediction by Inverse Virtual Screening

inferred← citeshttps://doi.org/10.1021/ci500131xopenalex-snapshot

Benchmark Data Sets for Structure-Based Computational Target Prediction

inferred← citeshttps://doi.org/10.1021/ci9002415openalex-snapshot

Conformational Sampling for Large-Scale Virtual Screening: Accuracy versus Ensemble Size

inferred← citeshttps://doi.org/10.1088/1742-6596/180/1/012053openalex-snapshot

FastBit: interactively searching massive data

inferred← citeshttps://doi.org/10.1093/bib/bbx047openalex-snapshot

Advances in computational approaches in identifying synergistic drug combinations

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ProteinsPlus: a comprehensive collection of web-based molecular modeling tools

inferred← citeshttps://doi.org/10.1109/cec.2010.5585932openalex-snapshot

Simplified chain folding models as metaheuristic benchmark for tuning real protein folding algorithms?

inferred← citeshttps://doi.org/10.1109/cluster.2011.11openalex-snapshot

BMF: Bitmapped Mass Fingerprinting for Fast Protein Identification

inferred← citeshttps://doi.org/10.1109/tvcg.2011.199openalex-snapshot

Feature-Based Statistical Analysis of Combustion Simulation Data

inferred← citeshttps://doi.org/10.1186/1758-2946-4-s1-p14openalex-snapshot

A flexible-hydrogen interaction model for protein-ligand docking

inferred← citeshttps://doi.org/10.1186/1758-2946-6-s1-o3openalex-snapshot

Facing the challenges of computational target prediction

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Biasing conformational ensembles towards bioactive-like conformers for ligand-based drug design

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Computational methods for the discovery of mood disorder therapies

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Integrating Virtual Screening and Combinatorial Chemistry for Accelerated Drug Discovery

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Molecular Docking: Challenges, Advances and its Use in Drug Discovery Perspective

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Molecular Shape Technologies in Drug Discovery: Methods and Applications

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Multi-target Phenylpropanoids Against Epilepsy

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Prediction of antiviral activity, cytotoxicity risks and molecular docking against HIV of constituents from marine algae

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