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Development and Evaluation of an Integrated Virtual Screening Strategy by Combining Molecular Docking and Pharmacophore Searching Based on Multiple Protein Structures

https://doi.org/10.1021/ci400382r
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What this work says

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

inferredcites →https://doi.org/10.1002/cmdc.200900314openalex-snapshot
Comparison of Structure‐ and Ligand‐Based Virtual Screening Protocols Considering Hit List Complementarity and Enrichment Factors
inferredcites →https://doi.org/10.1007/s00894-002-0101-1openalex-snapshot
ADME evaluation in drug discovery
inferredcites →https://doi.org/10.1016/j.ddtec.2013.02.002openalex-snapshot
Combination of ligand- and structure-based methods in virtual screening
inferredcites →https://doi.org/10.1016/j.drudis.2006.03.009openalex-snapshot
Consensus scoring for protein–ligand interactions
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.2009.01.003openalex-snapshot
Managing protein flexibility in docking and its applications
inferredcites →https://doi.org/10.1016/j.drudis.2010.06.011openalex-snapshot
Rho-kinase inhibition: a novel therapeutic target for the treatment of cardiovascular diseases
inferredcites →https://doi.org/10.1016/j.drudis.2013.01.007openalex-snapshot
The holistic integration of virtual screening in drug discovery
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/s0169-409x(00)00129-0openalex-snapshot
Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings 1PII of original article: S0169-409X(96)00423-1. The article was originally published in Advanced Drug Delivery Reviews 23 (1997) 3–25. 1
inferredcites →https://doi.org/10.1016/s0169-409x(96)00423-1openalex-snapshot
Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings
inferredcites →https://doi.org/10.1016/s1359-6446(02)02411-xopenalex-snapshot
Why do we need so many chemical similarity search methods?
inferredcites →https://doi.org/10.1016/s1359-6446(97)01163-xopenalex-snapshot
Virtual screening—an overview
inferredcites →https://doi.org/10.1016/s1367-5931(02)00341-1openalex-snapshot
Protein flexibility and drug design: how to hit a moving target
inferredcites →https://doi.org/10.1021/ci00020a020openalex-snapshot
Application of Genetic Function Approximation to Quantitative Structure-Activity Relationships and Quantitative Structure-Property Relationships
inferredcites →https://doi.org/10.1021/ci010113hopenalex-snapshot
A 3D Structure Database of Components from Chinese Traditional Medicinal Herbs
inferredcites →https://doi.org/10.1021/ci2004835openalex-snapshot
Virtual Screening Data Fusion Using Both Structure- and Ligand-Based Methods
inferredcites →https://doi.org/10.1021/ci300083ropenalex-snapshot
Protein–Ligand-Based Pharmacophores: Generation and Utility Assessment in Computational Ligand Profiling
inferredcites →https://doi.org/10.1021/ci300399wopenalex-snapshot
Consensus Docking: Improving the Reliability of Docking in a Virtual Screening Context
inferredcites →https://doi.org/10.1021/ci300547gopenalex-snapshot
Combination of Similarity Rankings Using Data Fusion
inferredcites →https://doi.org/10.1021/ci400059popenalex-snapshot
Hit Expansion Approaches Using Multiple Similarity Methods and Virtualized Query Structures
inferredcites →https://doi.org/10.1021/ci400065eopenalex-snapshot
Feasibility of Using Molecular Docking-Based Virtual Screening for Searching Dual Target Kinase Inhibitors
inferredcites →https://doi.org/10.1021/ci600343xopenalex-snapshot
ADME Evaluation in Drug Discovery. 7. Prediction of Oral Absorption by Correlation and Classification
inferredcites →https://doi.org/10.1021/ci6004993openalex-snapshot
Supervised Consensus Scoring for Docking and Virtual Screening
inferredcites →https://doi.org/10.1021/ci8003732openalex-snapshot
Consistent Improvement of Cross-Docking Results Using Binding Site Ensembles Generated with Elastic Network Normal Modes
inferredcites →https://doi.org/10.1021/ci900056copenalex-snapshot
Comparison of Several Molecular Docking Programs: Pose Prediction and Virtual Screening Accuracy
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/ci9004173openalex-snapshot
Multiple Pharmacophore Models Combined with Molecular Docking: A Reliable Way for Efficiently Identifying Novel PDE4 Inhibitors with High Structural Diversity
inferredcites →https://doi.org/10.1021/ja0469378openalex-snapshot
Incorporating Protein Flexibility in Structure-Based Drug Discovery: Using HIV-1 Protease as a Test Case
inferredcites →https://doi.org/10.1021/ja0709728openalex-snapshot
Exploring Experimental Sources of Multiple Protein Conformations in Structure-Based Drug Design
inferredcites →https://doi.org/10.1021/jm0203783openalex-snapshot
Comparative Evaluation of 11 Scoring Functions for Molecular Docking
inferredcites →https://doi.org/10.1021/jm030489hopenalex-snapshot
Assessing Scoring Functions for Protein−Ligand Interactions
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/jm050362nopenalex-snapshot
A Critical Assessment of Docking Programs and Scoring Functions
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/jm800562dopenalex-snapshot
Target Flexibility: An Emerging Consideration in Drug Discovery and Design
inferredcites →https://doi.org/10.1021/jm9602928openalex-snapshot
The Properties of Known Drugs. 1. Molecular Frameworks
inferredcites →https://doi.org/10.1021/jp003919dopenalex-snapshot
Evaluation and Reparametrization of the OPLS-AA Force Field for Proteins via Comparison with Accurate Quantum Chemical Calculations on Peptides
inferredcites →https://doi.org/10.1021/mp100465qopenalex-snapshot
ADME Evaluation in Drug Discovery. 10. Predictions of P-Glycoprotein Inhibitors Using Recursive Partitioning and Naive Bayesian Classification Techniques
inferredcites →https://doi.org/10.1021/mp300023xopenalex-snapshot
ADMET Evaluation in Drug Discovery. 12. Development of Binary Classification Models for Prediction of hERG Potassium Channel Blockage
inferredcites →https://doi.org/10.1021/mp300198dopenalex-snapshot
Drug-likeness Analysis of Traditional Chinese Medicines: Prediction of Drug-likeness Using Machine Learning Approaches
inferredcites →https://doi.org/10.1038/nrd1719openalex-snapshot
Rho kinase, a promising drug target for neurological disorders
inferredcites →https://doi.org/10.1038/nrd941openalex-snapshot
Integration of virtual and high-throughput screening
inferredcites →https://doi.org/10.1039/c2cs35357aopenalex-snapshot
Drug repositioning by structure-based virtual screening
inferredcites →https://doi.org/10.1074/jbc.270.49.29051openalex-snapshot
A Novel Serine/Threonine Kinase Binding the Ras-related RhoA GTPase Which Translocates the Kinase to Peripheral Membranes
inferredcites →https://doi.org/10.1093/nar/28.1.235openalex-snapshot
The Protein Data Bank
inferredcites →https://doi.org/10.1093/nar/gkl999openalex-snapshot
BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities
inferredcites →https://doi.org/10.1158/0008-5472.can-09-1541openalex-snapshot
Inhibition of Rho-Associated Kinase Signaling Prevents Breast Cancer Metastasis to Human Bone
inferredcites →https://doi.org/10.1177/1087057105281365openalex-snapshot
Using Extended-Connectivity Fingerprints with Laplacian-Modified Bayesian Analysis in High-Throughput Screening Follow-Up
inferredcites →https://doi.org/10.1186/1758-2946-3-29openalex-snapshot
Multiple search methods for similarity-based virtual screening: analysis of search overlap and precision
inferredcites →https://doi.org/10.1186/1758-2946-4-31openalex-snapshot
Drug-likeness analysis of traditional Chinese medicines: 1. property distributions of drug-like compounds, non-drug-like compounds and natural compounds from traditional Chinese medicines
inferredcites →https://doi.org/10.2147/tcrm.s2907openalex-snapshot
The therapeutic effects of Rho-ROCK inhibitors on CNS disorders
inferredcites →https://doi.org/10.2174/1381612043452721openalex-snapshot
Recent Development and Application of Virtual Screening in Drug Discovery: An Overview
inferredcites →https://doi.org/10.2174/157340908785747447openalex-snapshot
Combining Ligand- and Structure-Based Methods in Drug Design Projects
inferredcites →https://doi.org/10.2174/157340911796504305openalex-snapshot
New Features that Improve the Pharmacophore Tools from Accelrys
inferredcites →https://doi.org/10.4155/fmc.11.18openalex-snapshot
Integrating Structure-Based and Ligand-Based Approaches for Computational Drug Design

What points at this work

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

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A Multi‐complex Virtual Screening Approach Exploring Machine Learning to Identify Potential PI3Kγ Inhibitors
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Comparing pharmacophore models derived from crystallography and NMR ensembles
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A multi-conformational virtual screening approach based on machine learning targeting PI3Kγ
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Optimization of virtual screening against phosphoinositide 3-kinase delta: Integration of common feature pharmacophore and multicomplex-based molecular docking
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From virtual screening to reality: Identifying potent PI3Kγ inhibitors for inflammation treatment by harnessing machine learning and biological validation
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A combination of MD-derived pharmacophores and structure-based strategy identifies dual allosteric inhibitors of NS2B-NS3 proteases in Zika and West Nile viruses
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Computational and experimental prediction of molecules involved in the anti-melanoma action of berberine
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A Decade of Indonesian Atmosphere in Computer-Aided Drug Design
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HybridDock: A Hybrid Protein–Ligand Docking Protocol Integrating Protein- and Ligand-Based Approaches
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