Prediction, Analysis, and Comparison of Active Sites
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Matthias Rarey | Stefan Bietz | Andrea Volkamer | Mathias M. von Behren | M. Rarey | Andrea Volkamer | Stefan Bietz
[1] Nathanael Weill,et al. Alignment-Free Ultra-High-Throughput Comparison of Druggable Protein-Ligand Binding Sites , 2010, J. Chem. Inf. Model..
[2] Thomas L. Madden,et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.
[3] M. Sternberg,et al. Automated structure-based prediction of functional sites in proteins: applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking. , 2001, Journal of molecular biology.
[4] Terri K. Attwood,et al. The PRINTS Database: A Resource for Identification of Protein Families , 2002, Briefings Bioinform..
[5] Salim Bougouffa,et al. SitesIdentify: a protein functional site prediction tool , 2009, BMC Bioinformatics.
[6] C. Sander,et al. The FSSP database of structurally aligned protein fold families. , 1994, Nucleic acids research.
[7] Jian Peng,et al. Alignment of distantly related protein structures: algorithm, bound and implications to homology modeling , 2011, Bioinform..
[8] Andrzej Joachimiak,et al. Protein Functional Surfaces: Global Shape Matching and Local Spatial Alignments of Ligand Binding Sites , 2008, BMC Structural Biology.
[9] Dima Kozakov,et al. BIOINFORMATICS APPLICATIONS NOTE , 2022 .
[10] J. Thornton,et al. A method for localizing ligand binding pockets in protein structures , 2005, Proteins.
[11] M. Swindells,et al. Protein clefts in molecular recognition and function. , 1996, Protein science : a publication of the Protein Society.
[12] Janet M. Thornton,et al. Detection of 3D atomic similarities and their use in the discrimination of small molecule protein-binding sites , 2008, ECCB.
[13] Charles C. Persinger,et al. How to improve R&D productivity: the pharmaceutical industry's grand challenge , 2010, Nature Reviews Drug Discovery.
[14] Didier Rognan,et al. How to Measure the Similarity Between Protein Ligand-Binding Sites? , 2008 .
[15] F. Javier Luque,et al. MDpocket: open-source cavity detection and characterization on molecular dynamics trajectories , 2011, Bioinform..
[16] R. Hillig,et al. A structural biology view of target drugability , 2008, Expert opinion on drug discovery.
[17] Amos Bairoch,et al. PROSITE: A Documented Database Using Patterns and Profiles as Motif Descriptors , 2002, Briefings Bioinform..
[18] L. Johnson,et al. Protein kinase inhibition by staurosporine revealed in details of the molecular interaction with CDK2 , 1997, Nature Structural Biology.
[19] Julie C. Mitchell,et al. CryptoSite: Expanding the Druggable Proteome by Characterization and Prediction of Cryptic Binding Sites. , 2016, Journal of molecular biology.
[20] Dima Kozakov,et al. Fragment-based identification of druggable 'hot spots' of proteins using Fourier domain correlation techniques , 2009, Bioinform..
[21] Jie Wu,et al. BSSF: a fingerprint based ultrafast binding site similarity search and function analysis server , 2010, BMC Bioinformatics.
[22] Mona Singh,et al. Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure , 2009, PLoS Comput. Biol..
[23] Richard A. Ward,et al. Using protein-ligand docking to assess the chemical tractability of inhibiting a protein target , 2010, Journal of molecular modeling.
[24] G. Klebe,et al. From the Similarity Analysis of Protein Cavities to the Functional Classification of Protein Families Using Cavbase , 2006, Journal of Molecular Biology.
[25] J F Gibrat,et al. Surprising similarities in structure comparison. , 1996, Current opinion in structural biology.
[26] Rutger H A Folmer,et al. Fragment screening to predict druggability (ligandability) and lead discovery success. , 2011, Drug discovery today.
[27] Friedrich Rippmann,et al. TRAPP: A Tool for Analysis of Transient Binding Pockets in Proteins , 2013, J. Chem. Inf. Model..
[28] N. Ben-Tal,et al. ConSurf: an algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information. , 2001, Journal of molecular biology.
[29] Dusanka Janezic,et al. ProBiS-2012: web server and web services for detection of structurally similar binding sites in proteins , 2012, Nucleic Acids Res..
[30] H. Wolfson,et al. Recognition of Functional Sites in Protein Structures☆ , 2004, Journal of Molecular Biology.
[31] P. Hajduk,et al. Predicting protein druggability. , 2005, Drug discovery today.
[32] M. Jambon,et al. A new bioinformatic approach to detect common 3D sites in protein structures , 2003, Proteins.
[33] Matthias Rarey,et al. Exploiting structural information for drug-target assessment. , 2014, Future medicinal chemistry.
[34] Michal Brylinski,et al. FINDSITE: a combined evolution/structure-based approach to protein function prediction , 2009, Briefings Bioinform..
[35] Stefan Schmitt,et al. DrugPred: A Structure-Based Approach To Predict Protein Druggability Developed Using an Extensive Nonredundant Data Set , 2011, J. Chem. Inf. Model..
[36] Pieter F. W. Stouten,et al. Fast prediction and visualization of protein binding pockets with PASS , 2000, J. Comput. Aided Mol. Des..
[37] A. Elofsson,et al. Structure is three to ten times more conserved than sequence—A study of structural response in protein cores , 2009, Proteins.
[38] Ruben Abagyan,et al. Pocketome: an encyclopedia of small-molecule binding sites in 4D , 2011, Nucleic Acids Res..
[39] R. Wade,et al. Computational approaches to identifying and characterizing protein binding sites for ligand design , 2009, Journal of molecular recognition : JMR.
[40] Gabriele Cruciani,et al. A Common Reference Framework for Analyzing/Comparing Proteins and Ligands. Fingerprints for Ligands And Proteins (FLAP): Theory and Application , 2007, J. Chem. Inf. Model..
[41] E. Myers,et al. Basic local alignment search tool. , 1990, Journal of molecular biology.
[42] David C. Jones,et al. CATH--a hierarchic classification of protein domain structures. , 1997, Structure.
[43] Herbert Edelsbrunner,et al. Three-dimensional alpha shapes , 1994, ACM Trans. Graph..
[44] T. Kawabata. Detection of multiscale pockets on protein surfaces using mathematical morphology , 2010, Proteins.
[45] J. Thornton,et al. Tess: A geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites , 1997, Protein science : a publication of the Protein Society.
[46] D. Levitt,et al. POCKET: a computer graphics method for identifying and displaying protein cavities and their surrounding amino acids. , 1992, Journal of molecular graphics.
[47] Jan M. Kriegl,et al. Form follows function: Shape analysis of protein cavities for receptor‐based drug design , 2009, Proteomics.
[48] T. N. Bhat,et al. The Protein Data Bank , 2000, Nucleic Acids Res..
[49] C. Frömmel,et al. The automatic search for ligand binding sites in proteins of known three-dimensional structure using only geometric criteria. , 1996, Journal of molecular biology.
[50] E. Kellenberger,et al. A simple and fuzzy method to align and compare druggable ligand‐binding sites , 2008, Proteins.
[51] Friedrich Rippmann,et al. Perturbation Approaches for Exploring Protein Binding Site Flexibility to Predict Transient Binding Pockets. , 2016, Journal of chemical theory and computation.
[52] K. Kinoshita,et al. Identification of protein functions from a molecular surface database, eF-site , 2004, Journal of Structural and Functional Genomics.
[53] A. Hopkins,et al. The druggable genome , 2002, Nature Reviews Drug Discovery.
[54] Daniel Kuhn,et al. Combining Global and Local Measures for Structure-Based Druggability Predictions , 2012, J. Chem. Inf. Model..
[55] Itay Mayrose,et al. Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues , 2002, ISMB.
[56] Vincent Le Guilloux,et al. fpocket: online tools for protein ensemble pocket detection and tracking , 2010, Nucleic Acids Res..
[57] Robin Taylor,et al. A new test set for validating predictions of protein–ligand interaction , 2002, Proteins.
[58] Richard M. Jackson,et al. Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites , 2005, Bioinform..
[59] Yong Zhou,et al. Roll: a new algorithm for the detection of protein pockets and cavities with a rolling probe sphere , 2010, Bioinform..
[60] M. Jacobson,et al. Binding-Site Assessment by Virtual Fragment Screening , 2010, PloS one.
[61] E. Birney,et al. Pfam: the protein families database , 2013, Nucleic Acids Res..
[62] G. Superti-Furga,et al. Rediscovering the sweet spot in drug discovery. , 2003, Drug discovery today.
[63] Didier Rognan,et al. sc-PDB: an Annotated Database of Druggable Binding Sites from the Protein Data Bank , 2006, J. Chem. Inf. Model..
[64] Jan Griebsch,et al. PAST: fast structure-based searching in the PDB , 2006, Nucleic Acids Res..
[65] G. Klebe,et al. A new method to detect related function among proteins independent of sequence and fold homology. , 2002, Journal of molecular biology.
[66] Kesheng Wu,et al. FastBit: An Efficient Indexing Technology For Accelerating Data-Intensive Science , 2005 .
[67] Patrice Koehl,et al. The ASTRAL Compendium in 2004 , 2003, Nucleic Acids Res..
[68] Timo Krotzky,et al. Acceleration of Binding Site Comparisons by Graph Partitioning , 2015, Molecular informatics.
[69] Robert P. Sheridan,et al. Drug-like Density: A Method of Quantifying the "Bindability" of a Protein Target Based on a Very Large Set of Pockets and Drug-like Ligands from the Protein Data Bank , 2010, J. Chem. Inf. Model..
[70] M. Schroeder,et al. LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation , 2006, BMC Structural Biology.
[71] Janet M. Thornton,et al. Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons , 2005, Bioinform..
[72] R. Laskowski. SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions. , 1995, Journal of molecular graphics.
[73] Ming-Jing Hwang,et al. Ligand-binding site prediction using ligand-interacting and binding site-enriched protein triangles , 2012, Bioinform..
[74] B. Honig,et al. On the nature of cavities on protein surfaces: Application to the identification of drug‐binding sites , 2006, Proteins.
[75] Timo Krotzky,et al. Large-Scale Mining for Similar Protein Binding Pockets: With RAPMAD Retrieval on the Fly Becomes Real , 2015, J. Chem. Inf. Model..
[76] Bingding Huang,et al. MetaPocket: a meta approach to improve protein ligand binding site prediction. , 2009, Omics : a journal of integrative biology.
[77] R. Abagyan,et al. Pocketome via Comprehensive Identification and Classification of Ligand Binding Envelopes* , 2005, Molecular & Cellular Proteomics.
[78] Julien Michel,et al. A Collective Variable for the Rapid Exploration of Protein Druggability. , 2015, Journal of chemical theory and computation.
[79] Renxiao Wang,et al. The PDBbind database: collection of binding affinities for protein-ligand complexes with known three-dimensional structures. , 2004, Journal of medicinal chemistry.
[80] Matthias Rarey,et al. Fast Protein Binding Site Comparison via an Index-Based Screening Technology , 2013, J. Chem. Inf. Model..
[81] Lingna Hu,et al. Effects of Hinge-region Natural Polymorphisms on Human Immunodeficiency Virus-Type 1 Protease Structure, Dynamics, and Drug Pressure Evolution* , 2016, The Journal of Biological Chemistry.
[82] H. Edelsbrunner,et al. Anatomy of protein pockets and cavities: Measurement of binding site geometry and implications for ligand design , 1998, Protein science : a publication of the Protein Society.
[83] P. Hajduk,et al. Druggability indices for protein targets derived from NMR-based screening data. , 2005, Journal of medicinal chemistry.
[84] Harald Schwalbe,et al. Perspectives on NMR in drug discovery: a technique comes of age , 2008, Nature Reviews Drug Discovery.
[85] M Hendlich,et al. LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins. , 1997, Journal of molecular graphics & modelling.
[86] Jean-Michel Claverie,et al. Phydbac "Gene Function Predictor" : a gene annotation tool based on genomic context analysis , 2005, BMC Bioinformatics.
[87] Thomas A. Halgren,et al. Identifying and Characterizing Binding Sites and Assessing Druggability , 2009, J. Chem. Inf. Model..
[88] X. Barril. Druggability predictions: methods, limitations, and applications , 2013 .
[89] Y. Matsuo,et al. Method for comparing the structures of protein ligand‐binding sites and application for predicting protein–drug interactions , 2008, Proteins.
[90] Yu Li,et al. Identification of cavities on protein surface using multiple computational approaches for drug binding site prediction , 2011, Bioinform..
[91] Ivet Bahar,et al. Druggability Assessment of Allosteric Proteins by Dynamics Simulations in the Presence of Probe Molecules , 2012, Journal of Chemical Theory and Computation.
[92] R. Jackson,et al. Towards a structural classification of phosphate binding sites in protein–nucleotide complexes: An automated all‐against‐all structural comparison using geometric matching , 2004, Proteins.
[93] M. Milik,et al. Common Structural Cliques: a tool for protein structure and function analysis. , 2003, Protein engineering.
[94] G. Schneider,et al. PocketPicker: analysis of ligand binding-sites with shape descriptors , 2007, Chemistry Central Journal.
[95] Patric R. J. Östergård,et al. A fast algorithm for the maximum clique problem , 2002, Discret. Appl. Math..
[96] Hong Yan,et al. Alpha shape and Delaunay triangulation in studies of protein-related interactions , 2014, Briefings Bioinform..
[97] Matthias Rarey,et al. ASCONA: Rapid Detection and Alignment of Protein Binding Site Conformations , 2015, J. Chem. Inf. Model..
[98] Kalidas Yeturu,et al. PocketMatch: A new algorithm to compare binding sites in protein structures , 2008, BMC Bioinformatics.
[99] M. Rarey,et al. SIENA: Efficient Compilation of Selective Protein Binding Site Ensembles , 2016, J. Chem. Inf. Model..
[100] Y. Z. Chen,et al. Therapeutic Targets: Progress of Their Exploration and Investigation of Their Characteristics , 2006, Pharmacological Reviews.
[101] Russ B. Altman,et al. Using Multiple Microenvironments to Find Similar Ligand-Binding Sites: Application to Kinase Inhibitor Binding , 2011, PLoS Comput. Biol..
[102] Didier Rognan,et al. Comparison and Druggability Prediction of Protein-Ligand Binding Sites from Pharmacophore-Annotated Cavity Shapes , 2012, J. Chem. Inf. Model..
[103] K. Sjölander,et al. FlowerPower: clustering proteins into domain architecture classes for phylogenomic inference of protein function , 2007, BMC evolutionary biology.
[104] Yu Zong Chen,et al. Support vector machines approach for predicting druggable proteins: recent progress in its exploration and investigation of its usefulness. , 2007, Drug discovery today.
[105] Vincent Le Guilloux,et al. Fpocket: An open source platform for ligand pocket detection , 2009, BMC Bioinformatics.
[106] Eyke Hüllermeier,et al. Extended Graph-Based Models for Enhanced Similarity Search in Cavbase , 2014, IEEE/ACM Transactions on Computational Biology and Bioinformatics.
[107] Adam Godzik,et al. Flexible structure alignment by chaining aligned fragment pairs allowing twists , 2003, ECCB.
[108] Tuomo Kalliokoski,et al. Subpocket Analysis Method for Fragment-Based Drug Discovery , 2013, J. Chem. Inf. Model..
[109] G. Kellogg,et al. A novel and efficient tool for locating and characterizing protein cavities and binding sites , 2010, Proteins.
[110] Daniel R. Caffrey,et al. Structure-based maximal affinity model predicts small-molecule druggability , 2007, Nature Biotechnology.
[111] C. Ehrt,et al. Impact of Binding Site Comparisons on Medicinal Chemistry and Rational Molecular Design. , 2016, Journal of medicinal chemistry.
[112] H. Gohlke,et al. Structure-based computational analysis of protein binding sites for function and druggability prediction. , 2012, Journal of biotechnology.
[113] X. Barril,et al. Understanding and predicting druggability. A high-throughput method for detection of drug binding sites. , 2010, Journal of medicinal chemistry.
[114] Sourav Das,et al. Rapid Comparison of Protein Binding Site Surfaces with Property Encoded Shape Distributions , 2009, J. Chem. Inf. Model..
[115] Matthias Rarey,et al. Analyzing the Topology of Active Sites: On the Prediction of Pockets and Subpockets , 2010, J. Chem. Inf. Model..
[116] Shuangye Yin,et al. Fast screening of protein surfaces using geometric invariant fingerprints , 2009, Proceedings of the National Academy of Sciences.
[117] Carl J. Schmidt,et al. GoFigure: Automated Gene OntologyTM annotation , 2003, Bioinform..
[118] Daisuke Kihara,et al. Structure- and sequence-based function prediction for non-homologous proteins , 2012, Journal of Structural and Functional Genomics.
[119] Tina Ritschel,et al. Pharmacophore Fingerprint-Based Approach to Binding Site Subpocket Similarity and Its Application to Bioisostere Replacement , 2012, J. Chem. Inf. Model..
[120] N. Ben-Tal,et al. The ConSurf‐HSSP database: The mapping of evolutionary conservation among homologs onto PDB structures , 2004, Proteins.
[121] J M Thornton,et al. Derivation of 3D coordinate templates for searching structural databases: Application to ser‐His‐Asp catalytic triads in the serine proteinases and lipases , 1996, Protein science : a publication of the Protein Society.
[122] Jonathan Weiss,et al. Development of a Rule-Based Method for the Assessment of Protein Druggability , 2012, J. Chem. Inf. Model..
[123] Shmuel Pietrokovski,et al. Increased coverage of protein families with the Blocks Database servers , 2000, Nucleic Acids Res..
[124] Daniel Kuhn,et al. Predicting enzymatic function from global binding site descriptors , 2013, Proteins.