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Progress toward virtual screening for drug side effects

https://doi.org/10.1002/prot.10186
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What this work says

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

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Ligand-protein inverse docking and its potential use in the computer search of protein targets of a small molecule
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Optimizing the hydrogen‐bond network in Poisson–Boltzmann equation‐based pKa calculations
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Principles of Nucleic Acid Structure
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Principles of Nucleic Acid Structure
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Inhibitor Binding to Active and Inactive CDK2
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Intracellular targets of cyclin-dependent kinase inhibitors: identification by affinity chromatography using immobilised inhibitors
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Detailed Analysis of Scoring Functions for Virtual Screening
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All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins
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Deciphering common failures in molecular docking of ligand-protein complexes
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High-throughput screening approaches for investigating drug metabolism and pharmacokinetics
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The Protein Data Bank
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The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000
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What points at this work

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

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Analysis of Pharmacology Data and the Prediction of Adverse Drug Reactions and Off‐Target Effects from Chemical Structure
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Structure‐Based Approaches to Target Fishing and Ligand Profiling
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Current Awareness: Pharmacoepidemiology and Drug Safety
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From Molecular Modeling to Drug Design
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Multiple ligand-binding modes in bacterial R67 dihydrofolate reductase
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Docking-based inverse virtual screening: methods, applications, and challenges
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Comparative Modeling of Drug Target Proteins
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Comparative Modeling of Drug Target Proteins☆
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Inhibition studies with rationally designed inhibitors of the human low molecular weight protein tyrosine phosphatase
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Structural basis for the GSK-3β binding affinity and selectivity against CDK-2 of 1-(4-aminofurazan-3yl)-5-dialkylaminomethyl-1H-[1,2,3] triazole-4-carboxylic acid derivatives
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A structural comparative approach to identifying novel antimalarial inhibitors
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Electrostatic Potential of Nucleotide-free Protein is Sufficient for Discrimination Between Adenine and Guanine-specific Binding Sites
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Structure-based systems biology for analyzing off-target binding
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Comparative Protein Structure Modeling and its Applications to Drug Discovery
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What is the relevance of bioinformatics to pharmacology?
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Predicting undesirable drug interactions with promiscuous proteins in silico
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Reengineering the pharmaceutical industry by crash-testing molecules
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Chapter 13 Targeting the Kinome with Computational Chemistry
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Rapid Identification of Inhibitors and Prediction of Ligand Selectivity for Multiple Proteins: Application to Protein Kinases
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A Comprehensive Docking Study on the Selectivity of Binding of Aromatic Compounds to Proteins
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Virtual Target Screening: Validation Using Kinase Inhibitors
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GlamDock: Development and Validation of a New Docking Tool on Several Thousand Protein−Ligand Complexes
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LEA3D: A Computer-Aided Ligand Design for Structure-Based Drug Design
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Rapid Computational Identification of the Targets of Protein Kinase Inhibitors
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Ligand selectivity and competition between enzymes in silico
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AMDE: a novel attention-mechanism-based multidimensional feature encoder for drug–drug interaction prediction
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kinDOCK: a tool for comparative docking of protein kinase ligands
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Prediction of Torsade-Causing Potential of Drugs by Support Vector Machine Approach No funding was used to assist in conducting the study and the authors do not have any conflicts of interest directly relevant to the contents of the manuscript.
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Efficient Knowledge Graph Embedding Framework to Alleviate Data Sparsity for Polypharmacy Side Effects Prediction
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Druggability of Coronary Artery Disease Risk Loci
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In Silico Elucidation of the Molecular Mechanism Defining the Adverse Effect of Selective Estrogen Receptor Modulators
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In Silico Elucidation of the Molecular Mechanism Defining the Adverse Effect of Selective Estrogen Receptor Modulators
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Prediction of Putative Adverse Drug Reaction-Related Proteins from Primary Sequence by Support Vector Machines
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Predicting the structure and energetics of protein-ligand interaction
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