CFam: a chemical families database based on iterative selection of functional seeds and seed-directed compound clustering
暂无分享,去创建一个
Zhe Chen | Feng Xu | Cheng Zhang | Sheng-Yong Yang | Yu Zong Chen | Lin Tao | Xian Zeng | Peng Zhang | Chu Qin | Shangying Chen | Y. Chen | Feng Xu | L. Tao | C. Qin | S. Chen | X. Zeng | Peng Zhang | Zhe Chen | S. Yang | Cheng Zhang | Lin Tao | Xian Zeng | Chu Qin
[1] George Papadatos,et al. The ChEMBL bioactivity database: an update , 2013, Nucleic Acids Res..
[2] Ryan G. Coleman,et al. ZINC: A Free Tool to Discover Chemistry for Biology , 2012, J. Chem. Inf. Model..
[3] E. Birney,et al. Pfam: the protein families database , 2013, Nucleic Acids Res..
[4] Herbert Waldmann,et al. Biology-oriented synthesis: harnessing the power of evolution. , 2014, Journal of the American Chemical Society.
[5] Ian Sillitoe,et al. Extending CATH: increasing coverage of the protein structure universe and linking structure with function , 2010, Nucleic Acids Res..
[6] Sereina Riniker,et al. Heterogeneous Classifier Fusion for Ligand-Based Virtual Screening: Or, How Decision Making by Committee Can Be a Good Thing , 2013, J. Chem. Inf. Model..
[7] Gemma L Thomas,et al. Natural product-like synthetic libraries. , 2011, Current opinion in chemical biology.
[8] Yossef Kliger,et al. Improving Classical Substructure-Based Virtual Screening to Handle Extrapolation Challenges , 2012, J. Chem. Inf. Model..
[9] Christian Lemmen,et al. Similarity searching and scaffold hopping in synthetically accessible combinatorial chemistry spaces. , 2008, Journal of medicinal chemistry.
[10] Gisbert Schneider,et al. NIPALSTREE: A New Hierarchical Clustering Approach for Large Compound Libraries and Its Application to Virtual Screening , 2006, J. Chem. Inf. Model..
[11] R. Durbin,et al. Pfam: A comprehensive database of protein domain families based on seed alignments , 1997, Proteins.
[12] Weizhong Li. A Fast Clustering Algorithm for Analyzing Highly Similar Compounds of Very Large Libraries , 2006, J. Chem. Inf. Model..
[13] Jürgen Bajorath,et al. Development of a Compound Class-Directed Similarity Coefficient That Accounts for Molecular Complexity Effects in Fingerprint Searching , 2009, J. Chem. Inf. Model..
[14] Jürgen Bajorath,et al. Rationalizing Structure and Target Relationships between Current Drugs , 2012, The AAPS Journal.
[15] Gisbert Schneider,et al. A Hierarchical Clustering Approach for Large Compound Libraries , 2005, J. Chem. Inf. Model..
[16] Stefan Wetzel,et al. Interactive exploration of chemical space with Scaffold Hunter. , 2009, Nature chemical biology.
[17] CHUN WEI YAP,et al. PaDEL‐descriptor: An open source software to calculate molecular descriptors and fingerprints , 2011, J. Comput. Chem..
[18] Alan Bridge,et al. New and continuing developments at PROSITE , 2012, Nucleic Acids Res..
[19] Jacek Tabor,et al. Asymmetric Clustering Index in a Case Study of 5-HT1A Receptor Ligands , 2014, PloS one.
[20] P. M. Dean,et al. Molecular Similarity in Drug Design , 2007 .
[21] P. Willett,et al. Promoting Access to White Rose Research Papers Similarity-based Virtual Screening Using 2d Fingerprints , 2022 .
[22] Peter Willett,et al. Similarity-based virtual screening using 2D fingerprints. , 2006, Drug discovery today.
[23] Jürgen Bajorath,et al. Anatomy of Fingerprint Search Calculations on Structurally Diverse Sets of Active Compounds , 2005, J. Chem. Inf. Model..
[24] N. Nikolova,et al. International Union of Pure and Applied Chemistry, LUMO energy ± The Lowest Unoccupied Molecular Orbital (LUMO) , 2022 .
[25] R. Glen,et al. Molecular similarity: a key technique in molecular informatics. , 2004, Organic & biomolecular chemistry.
[26] Stefan Wetzel,et al. Charting, navigating, and populating natural product chemical space for drug discovery. , 2012, Journal of medicinal chemistry.
[27] Vincent Le Guilloux,et al. Visual Characterization and Diversity Quantification of Chemical Libraries: 1. Creation of Delimited Reference Chemical Subspaces , 2011, J. Chem. Inf. Model..
[28] Jürgen Bajorath,et al. Database Searching for Compounds with Similar Biological Activity Using Short Binary Bit String Representations of Molecules , 1999, J. Chem. Inf. Comput. Sci..
[29] Gabriele Cruciani,et al. Suitability of molecular descriptors for database mining. A comparative analysis. , 2002, Journal of medicinal chemistry.
[30] Chris Morley,et al. Open Babel: An open chemical toolbox , 2011, J. Cheminformatics.
[31] Michael T. M. Emmerich,et al. A novel chemogenomics analysis of G protein-coupled receptors (GPCRs) and their ligands: a potential strategy for receptor de-orphanization , 2010, BMC Bioinformatics.
[32] Y. Martin,et al. Do structurally similar molecules have similar biological activity? , 2002, Journal of medicinal chemistry.
[33] Gerhard Klebe,et al. Successful virtual screening for novel inhibitors of human carbonic anhydrase: strategy and experimental confirmation. , 2002, Journal of medicinal chemistry.
[34] Dimitris K. Agrafiotis,et al. A Cluster-Based Strategy for Assessing the Overlap between Large Chemical Libraries and Its Application to a Recent Acquisition , 2006, J. Chem. Inf. Model..
[35] Stefan Günther,et al. SuperPred: drug classification and target prediction , 2008, Nucleic Acids Res..
[36] Feng Xu,et al. Therapeutic target database update 2014: a resource for targeted therapeutics , 2013, Nucleic Acids Res..
[37] Robert P Sheridan,et al. Why do we need so many chemical similarity search methods? , 2002, Drug discovery today.
[38] Yvonne C. Martin,et al. The Information Content of 2D and 3D Structural Descriptors Relevant to Ligand-Receptor Binding , 1997, J. Chem. Inf. Comput. Sci..
[39] G. Makara,et al. Measuring molecular similarity and diversity: total pharmacophore diversity. , 2001, Journal of medicinal chemistry.
[40] Guixia Liu,et al. Performance Evaluation of 2D Fingerprint and 3D Shape Similarity Methods in Virtual Screening , 2012, J. Chem. Inf. Model..
[41] Peter Willett,et al. Similarity Searching in Files of Three-Dimensional Chemical Structures: Analysis of the BIOSTER Database Using Two-Dimensional Fingerprints and Molecular Field Descriptors , 2000, J. Chem. Inf. Comput. Sci..
[42] Stefan Wetzel,et al. Bioactivity-guided mapping and navigation of chemical space. , 2009, Nature chemical biology.
[43] John M. Barnard,et al. Chemical Similarity Searching , 1998, J. Chem. Inf. Comput. Sci..
[44] David S. Wishart,et al. DrugBank 4.0: shedding new light on drug metabolism , 2013, Nucleic Acids Res..
[45] Tim J. P. Hubbard,et al. Data growth and its impact on the SCOP database: new developments , 2007, Nucleic Acids Res..
[46] Jürgen Bajorath,et al. Exploring structure–selectivity relationships of biogenic amine GPCR antagonists using similarity searching and dynamic compound mapping , 2008, Molecular Diversity.
[47] Yanli Wang,et al. PubChem: Integrated Platform of Small Molecules and Biological Activities , 2008 .
[48] Maria F. Sassano,et al. A Pharmacological Organization of G Protein-coupled Receptors , 2012, Nature Methods.
[49] J. Medina-Franco,et al. Expanding the medicinally relevant chemical space with compound libraries. , 2012, Drug discovery today.
[50] H. Matter,et al. Selecting optimally diverse compounds from structure databases: a validation study of two-dimensional and three-dimensional molecular descriptors. , 1997, Journal of medicinal chemistry.
[51] Robert D. Finn,et al. InterPro in 2011: new developments in the family and domain prediction database , 2011, Nucleic acids research.
[52] Tudor I. Oprea,et al. Cross-pharmacology analysis of G protein-coupled receptors. , 2011, Current topics in medicinal chemistry.
[53] A. Hopkins,et al. Navigating chemical space for biology and medicine , 2004, Nature.
[54] Robert J. Jilek,et al. "Lead hopping". Validation of topomer similarity as a superior predictor of similar biological activities. , 2004, Journal of medicinal chemistry.
[55] Jürgen Bajorath,et al. Molecular similarity analysis in virtual screening: foundations, limitations and novel approaches. , 2007, Drug discovery today.
[56] David S. Wishart,et al. HMDB 3.0—The Human Metabolome Database in 2013 , 2012, Nucleic Acids Res..
[57] Andreas Bender,et al. How Similar Are Similarity Searching Methods? A Principal Component Analysis of Molecular Descriptor Space , 2009, J. Chem. Inf. Model..
[58] Adam Godzik,et al. Clustering of highly homologous sequences to reduce the size of large protein databases , 2001, Bioinform..