标题
Identification of Similar Binding Sites to Detect Distant Polypharmacology
作者
关键词
-
出版物
Molecular Informatics
Volume 32, Issue 11-12, Pages 976-990
出版商
Wiley
发表日期
2013-10-18
DOI
10.1002/minf.201300082
参考文献
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注意:仅列出部分参考文献,下载原文获取全部文献信息。- APoc: large-scale identification of similar protein pockets
- (2013) Mu Gao et al. BIOINFORMATICS
- Fast Protein Binding Site Comparison via an Index-Based Screening Technology
- (2013) Mathias M. von Behren et al. Journal of Chemical Information and Modeling
- Subpocket Analysis Method for Fragment-Based Drug Discovery
- (2013) Tuomo Kalliokoski et al. Journal of Chemical Information and Modeling
- Chemoisosterism in the Proteome
- (2013) Xavier Jalencas et al. Journal of Chemical Information and Modeling
- A pharmacological organization of G protein–coupled receptors
- (2013) Henry Lin et al. NATURE METHODS
- Identification of Pim Kinases as Novel Targets for PJ34 with Confounding Effects in PARP Biology
- (2012) Albert A. Antolín et al. ACS Chemical Biology
- Chemogenomics in drug discovery: computational methods based on the comparison of binding sites
- (2012) Anna Vulpetti et al. Future Medicinal Chemistry
- Pharmacophore Fingerprint-Based Approach to Binding Site Subpocket Similarity and Its Application to Bioisostere Replacement
- (2012) David J. Wood et al. Journal of Chemical Information and Modeling
- Structural Insights into the Molecular Basis of the Ligand Promiscuity
- (2012) Noé Sturm et al. Journal of Chemical Information and Modeling
- Chemocentric Informatics Approach to Drug Discovery: Identification and Experimental Validation of Selective Estrogen Receptor Modulators as Ligands of 5-Hydroxytryptamine-6 Receptors and as Potential Cognition Enhancers
- (2012) Rima Hajjo et al. JOURNAL OF MEDICINAL CHEMISTRY
- Life Beyond Kinases: Structure-Based Discovery of Sorafenib as Nanomolar Antagonist of 5-HT Receptors
- (2012) Xingyu Lin et al. JOURNAL OF MEDICINAL CHEMISTRY
- Structure of the human κ-opioid receptor in complex with JDTic
- (2012) Huixian Wu et al. NATURE
- Crystal Structure of a Lipid G Protein-Coupled Receptor
- (2012) M. A. Hanson et al. SCIENCE
- On the origins of drug polypharmacology
- (2012) Xavier Jalencas et al. MedChemComm
- Strategies to Discover Unexpected Targets for Drugs Active at G Protein–Coupled Receptors
- (2011) John A. Allen et al. Annual Review of Pharmacology and Toxicology
- Novel Computational Approaches to Polypharmacology as a Means to Define Responses to Individual Drugs
- (2011) Lei Xie et al. Annual Review of Pharmacology and Toxicology
- Old friends in new guise: repositioning of known drugs with structural bioinformatics
- (2011) V. J. Haupt et al. BRIEFINGS IN BIOINFORMATICS
- Context-Based Identification of Protein-Protein Interfaces and “Hot-Spot” Residues
- (2011) Tim Geppert et al. CHEMISTRY & BIOLOGY
- Linking Pharmacology to Clinical Reports: Cyclobenzaprine and Its Possible Association With Serotonin Syndrome
- (2011) J Mestres et al. CLINICAL PHARMACOLOGY & THERAPEUTICS
- Cross-Pharmacology Analysis of G Protein-Coupled Receptors
- (2011) Ferran Brianso et al. CURRENT TOPICS IN MEDICINAL CHEMISTRY
- Multi-targeted activity of maslinic acid as an antimalarial natural compound
- (2011) Carlos Moneriz et al. FEBS Journal
- Divergence and Convergence in Enzyme Evolution
- (2011) Michael Y. Galperin et al. JOURNAL OF BIOLOGICAL CHEMISTRY
- Structure-based computational analysis of protein binding sites for function and druggability prediction
- (2011) Britta Nisius et al. JOURNAL OF BIOTECHNOLOGY
- Residue Preference Mapping of Ligand Fragments in the Protein Data Bank
- (2011) Lirong Wang et al. Journal of Chemical Information and Modeling
- CrystalDock: A Novel Approach to Fragment-Based Drug Design
- (2011) Jacob D. Durrant et al. Journal of Chemical Information and Modeling
- Large-Scale Evaluation of CavBase for Analyzing the Polypharmacology of Kinase Inhibitors
- (2011) Tuomo Kalliokoski et al. Molecular Informatics
- Structure of the human histamine H1 receptor complex with doxepin
- (2011) Tatsuro Shimamura et al. NATURE
- ChEMBL: a large-scale bioactivity database for drug discovery
- (2011) A. Gaulton et al. NUCLEIC ACIDS RESEARCH
- Structure-based discovery of prescription drugs that interact with the norepinephrine transporter, NET
- (2011) A. Schlessinger et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- PDB-scale analysis of known and putative ligand-binding sites with structural sketches
- (2011) Jun-Ichi Ito et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- Using Multiple Microenvironments to Find Similar Ligand-Binding Sites: Application to Kinase Inhibitor Binding
- (2011) Tianyun Liu et al. PLoS Computational Biology
- iAlign: a method for the structural comparison of protein–protein interfaces
- (2010) Mu Gao et al. BIOINFORMATICS
- ProBiS algorithm for detection of structurally similar protein binding sites by local structural alignment
- (2010) Janez Konc et al. BIOINFORMATICS
- A new protein binding pocket similarity measure based on comparison of clouds of atoms in 3D: application to ligand prediction
- (2010) Brice Hoffmann et al. BMC BIOINFORMATICS
- BSSF: a fingerprint based ultrafast binding site similarity search and function analysis server
- (2010) Bing Xiong et al. BMC BIOINFORMATICS
- Architectural Repertoire of Ligand-Binding Pockets on Protein Surfaces
- (2010) Martin Weisel et al. CHEMBIOCHEM
- In Silico Prediction of Binding Sites on Proteins
- (2010) Simon Leis et al. CURRENT MEDICINAL CHEMISTRY
- Druggable pockets and binding site centric chemical space: a paradigm shift in drug discovery
- (2010) Stéphanie Pérot et al. DRUG DISCOVERY TODAY
- Structural genomics—Impact on biomedicine and drug discovery
- (2010) Johan Weigelt EXPERIMENTAL CELL RESEARCH
- Predicting Polypharmacology by Binding Site Similarity: From Kinases to the Protein Universe
- (2010) Francesca Milletti et al. Journal of Chemical Information and Modeling
- Alignment-Free Ultra-High-Throughput Comparison of Druggable Protein−Ligand Binding Sites
- (2010) Nathanaël Weill et al. Journal of Chemical Information and Modeling
- Large-Scale Comparison of Four Binding Site Detection Algorithms
- (2010) Peter Schmidtke et al. Journal of Chemical Information and Modeling
- Analyzing the Topology of Active Sites: On the Prediction of Pockets and Subpockets
- (2010) Andrea Volkamer et al. Journal of Chemical Information and Modeling
- Chemical Fragments that Hydrogen Bond to Asp, Glu, Arg, and His Side Chains in Protein Binding Sites
- (2010) A.W. Edith Chan et al. JOURNAL OF MEDICINAL CHEMISTRY
- Prediction and Evaluation of Protein Farnesyltransferase Inhibition by Commercial Drugs
- (2010) Amanda J. DeGraw et al. JOURNAL OF MEDICINAL CHEMISTRY
- Self-Organizing Fuzzy Graphs for Structure-Based Comparison of Protein Pockets
- (2010) Felix Reisen et al. JOURNAL OF PROTEOME RESEARCH
- Drug-Target Networks
- (2010) Ingo Vogt et al. Molecular Informatics
- Structure-Based Approaches to Target Fishing and Ligand Profiling
- (2010) Didier Rognan Molecular Informatics
- Cross-Reactivity Virtual Profiling of the Human Kinome by X-ReactKIN: A Chemical Systems Biology Approach
- (2010) Michal Brylinski et al. MOLECULAR PHARMACEUTICS
- DrugBank 3.0: a comprehensive resource for 'Omics' research on drugs
- (2010) C. Knox et al. NUCLEIC ACIDS RESEARCH
- The RCSB Protein Data Bank: redesigned web site and web services
- (2010) P. W. Rose et al. NUCLEIC ACIDS RESEARCH
- Binding of Protein Kinase Inhibitors to Synapsin I Inferred from Pair-Wise Binding Site Similarity Measurements
- (2010) Enrico De Franchi et al. PLoS One
- Superpose3D: A Local Structural Comparison Program That Allows for User-Defined Structure Representations
- (2010) Pier Federico Gherardini et al. PLoS One
- Real-time ligand binding pocket database search using local surface descriptors
- (2010) Rayan Chikhi et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- Structures of the CXCR4 Chemokine GPCR with Small-Molecule and Cyclic Peptide Antagonists
- (2010) B. Wu et al. SCIENCE
- Structure of the Human Dopamine D3 Receptor in Complex with a D2/D3 Selective Antagonist
- (2010) E. Y. T. Chien et al. SCIENCE
- A Multidimensional Strategy to Detect Polypharmacological Targets in the Absence of Structural and Sequence Homology
- (2010) Jacob D. Durrant et al. PLoS Computational Biology
- Prediction of sub-cavity binding preferences using an adaptive physicochemical structure representation
- (2009) I. Wallach et al. BIOINFORMATICS
- 3D-SURFER: software for high-throughput protein surface comparison and analysis
- (2009) David La et al. BIOINFORMATICS
- PocketMatch: A new algorithm to compare binding sites in protein structures
- (2009) Kalidas Yeturu et al. BMC BIOINFORMATICS
- Computational Fragment-Based Approach at PDB Scale by Protein Local Similarity
- (2009) Fabrice Moriaud et al. Journal of Chemical Information and Modeling
- Rapid Comparison of Protein Binding Site Surfaces with Property Encoded Shape Distributions
- (2009) Sourav Das et al. Journal of Chemical Information and Modeling
- Identifying and Characterizing Binding Sites and Assessing Druggability
- (2009) Thomas A. Halgren Journal of Chemical Information and Modeling
- The topology of drug–target interaction networks: implicit dependence on drug properties and target families
- (2009) Jordi Mestres et al. Molecular BioSystems
- Predicting new molecular targets for known drugs
- (2009) Michael J. Keiser et al. NATURE
- Protein promiscuity and its implications for biotechnology
- (2009) Irene Nobeli et al. NATURE BIOTECHNOLOGY
- An overview of the PubChem BioAssay resource
- (2009) Yanli Wang et al. NUCLEIC ACIDS RESEARCH
- MolLoc: a web tool for the local structural alignment of molecular surfaces
- (2009) S. Angaran et al. NUCLEIC ACIDS RESEARCH
- Model structure of APOBEC3C reveals a binding pocket modulating ribonucleic acid interaction required for encapsidation
- (2009) B. Stauch et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Fast screening of protein surfaces using geometric invariant fingerprints
- (2009) S. Yin et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Tess: A geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites
- (2009) Andrew C. Wallace et al. PROTEIN SCIENCE
- Comprehensive Structural Classification of Ligand-Binding Motifs in Proteins
- (2009) Akira R. Kinjo et al. STRUCTURE
- PSI-2: Structural Genomics to Cover Protein Domain Family Space
- (2009) Benoît H. Dessailly et al. STRUCTURE
- Harvesting Candidate Genes Responsible for Serious Adverse Drug Reactions from a Chemical-Protein Interactome
- (2009) Lun Yang et al. PLoS Computational Biology
- Drug Discovery Using Chemical Systems Biology: Repositioning the Safe Medicine Comtan to Treat Multi-Drug and Extensively Drug Resistant Tuberculosis
- (2009) Sarah L. Kinnings et al. PLoS Computational Biology
- Detection of 3D atomic similarities and their use in the discrimination of small molecule protein-binding sites
- (2008) R. Najmanovich et al. BIOINFORMATICS
- Massively Parallel Screening of the Receptorome
- (2008) Niels Jensen et al. COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING
- How to Measure the Similarity Between Protein Ligand-Binding Sites?
- (2008) Esther Kellenberger et al. Current Computer-Aided Drug Design
- Chemocavity: Specific Concavity in Protein Reserved for the Binding of Biologically Functional Small Molecules
- (2008) Shinji Soga et al. Journal of Chemical Information and Modeling
- Target Flexibility: An Emerging Consideration in Drug Discovery and Design†
- (2008) Pietro Cozzini et al. JOURNAL OF MEDICINAL CHEMISTRY
- Vicinity analysis: a methodology for the identification of similar protein active sites
- (2008) A. McGready et al. JOURNAL OF MOLECULAR MODELING
- Structure of a β1-adrenergic G-protein-coupled receptor
- (2008) Tony Warne et al. NATURE
- IUPHAR-DB: the IUPHAR database of G protein-coupled receptors and ion channels
- (2008) Anthony J. Harmar et al. NUCLEIC ACIDS RESEARCH
- Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments
- (2008) L. Xie et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- A simple and fuzzy method to align and compare druggable ligand-binding sites
- (2008) Claire Schalon et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- Rapid comparison of properties on protein surface
- (2008) Lee Sael et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- Method for comparing the structures of protein ligand-binding sites and application for predicting protein-drug interactions
- (2008) Ryoichi Minai et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- Drug Target Identification Using Side-Effect Similarity
- (2008) M. Campillos et al. SCIENCE
- Protein Functional Surfaces: Global Shape Matching and Local Spatial Alignments of Ligand Binding Sites
- (2008) T. ANDREW Binkowski et al. BMC STRUCTURAL BIOLOGY
- Binding similarity network of ligand
- (2007) Keunwan Park et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
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