Exploring structural diversity across the protein universe with The Encyclopedia of Domains.

Autor: Lau AM; Department of Computer Science, University College London, London WC1E 6BT, UK., Bordin N; Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, UK., Kandathil SM; Department of Computer Science, University College London, London WC1E 6BT, UK., Sillitoe I; Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, UK., Waman VP; Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, UK., Wells J; Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, UK.; Centre for Artificial Intelligence, University College London, London WC1V 6BH, UK., Orengo CA; Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, UK., Jones DT; Department of Computer Science, University College London, London WC1E 6BT, UK.; Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, UK.

Publikováno v: Science (New York, N.Y.) [Science] 2024 Nov; Vol. 386 (6721), pp. eadq4946. Date of Electronic Publication: 2024 Nov 01.

Clustering protein functional families at large scale with hierarchical approaches.

Autor: Bordin N; Institute of Structural and Molecular Biology, University College London, London, UK., Scholes H; Institute of Structural and Molecular Biology, University College London, London, UK., Rauer C; Institute of Structural and Molecular Biology, University College London, London, UK.; Universidad Autonoma de Madrid, Ciudad Universitaria de Cantoblanco, Madrid, Spain., Roca-Martínez J; Institute of Structural and Molecular Biology, University College London, London, UK., Sillitoe I; Institute of Structural and Molecular Biology, University College London, London, UK., Orengo C; Institute of Structural and Molecular Biology, University College London, London, UK.

Publikováno v: Protein science : a publication of the Protein Society [Protein Sci] 2024 Sep; Vol. 33 (9), pp. e5140.

Chainsaw: protein domain segmentation with fully convolutional neural networks.

Autor: Wells J; Centre for Artificial Intelligence, University College London, WC1E 6BT, United Kingdom., Hawkins-Hooker A; Centre for Artificial Intelligence, University College London, WC1E 6BT, United Kingdom., Bordin N; Institute of Structural and Molecular Biology, University College London, WC1E 6BT, United Kingdom., Sillitoe I; Institute of Structural and Molecular Biology, University College London, WC1E 6BT, United Kingdom., Paige B; Centre for Artificial Intelligence, University College London, WC1E 6BT, United Kingdom., Orengo C; Institute of Structural and Molecular Biology, University College London, WC1E 6BT, United Kingdom.

Publikováno v: Bioinformatics (Oxford, England) [Bioinformatics] 2024 May 02; Vol. 40 (5).

ModelCIF: An Extension of PDBx/mmCIF Data Representation for Computed Structure Models.

Autor: Vallat B; Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA. Electronic address: brinda.vallat@rcsb.org., Tauriello G; Biozentrum, University of Basel, Basel, Switzerland; Computational Structural Biology, SIB Swiss Institute of Bioinformatics, Basel, Switzerland., Bienert S; Biozentrum, University of Basel, Basel, Switzerland; Computational Structural Biology, SIB Swiss Institute of Bioinformatics, Basel, Switzerland., Haas J; Biozentrum, University of Basel, Basel, Switzerland; Computational Structural Biology, SIB Swiss Institute of Bioinformatics, Basel, Switzerland., Webb BM; Department of Bioengineering and Therapeutic Sciences, the Quantitative Biosciences Institute (QBI), and the Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94157, USA., Žídek A; DeepMind, London, UK., Zheng W; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA., Peisach E; Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA., Piehl DW; Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA., Anischanka I; Department of Biochemistry, and Institute for Protein Design, University of Washington, Seattle, WA 98195, USA., Sillitoe I; Department of Structural and Molecular Biology, UCL, London, UK., Tolchard J; AlphaFold Protein Structure Database, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK; Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK., Varadi M; AlphaFold Protein Structure Database, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK; Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK., Baker D; Department of Biochemistry, and Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA., Orengo C; Department of Structural and Molecular Biology, UCL, London, UK., Zhang Y; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA., Hoch JC; Biological Magnetic Resonance Data Bank, Department of Molecular Biology and Biophysics, University of Connecticut, Farmington, CT 06030, USA., Kurisu G; Protein Data Bank Japan, Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan., Patwardhan A; Electron Microscopy Data Bank, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK., Velankar S; AlphaFold Protein Structure Database, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK; Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK., Burley SK; Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA; Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, La Jolla, CA 92093, USA; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA., Sali A; Department of Bioengineering and Therapeutic Sciences, the Quantitative Biosciences Institute (QBI), and the Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94157, USA. Electronic address: https://twitter.com/salilab_ucsf., Schwede T; Biozentrum, University of Basel, Basel, Switzerland; Computational Structural Biology, SIB Swiss Institute of Bioinformatics, Basel, Switzerland., Berman HM; Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA., Westbrook JD; Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA.

Publikováno v: Journal of molecular biology [J Mol Biol] 2023 Jul 15; Vol. 435 (14), pp. 168021. Date of Electronic Publication: 2023 Feb 23.

InterPro in 2022.

Autor: Paysan-Lafosse T; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK., Blum M; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK., Chuguransky S; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK., Grego T; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK., Pinto BL; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK., Salazar GA; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK., Bileschi ML; Google Research, Brain team, Cambridge, MA, USA., Bork P; European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany.; Yonsei Frontier Lab (YFL), Yonsei University, 03722 Seoul, South Korea.; Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany., Bridge A; Swiss-Prot Group, Swiss Institute of Bioinformatics, CMU, 1 rue Michel Servet, CH-1211, Geneva 4, Switzerland., Colwell L; Google Research, Brain team, Cambridge, MA, USA.; Department of Chemistry, University of Cambridge, Cambridge, UK., Gough J; Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Ave, Trumpington, Cambridge CB2 0QH, UK., Haft DH; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA., Letunić I; Biobyte Solutions GmbH, Bothestr 142, 69126 Heidelberg, Germany., Marchler-Bauer A; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA., Mi H; Division of Bioinformatics, Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90033, USA., Natale DA; Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USA., Orengo CA; Department of Structural and Molecular Biology, University College London, Gower St, Bloomsbury, London WC1E 6BT, UK., Pandurangan AP; Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Ave, Trumpington, Cambridge CB2 0QH, UK.; Department of Biochemistry, Sanger Building, University of Cambridge, Cambridge, UK., Rivoire C; Swiss-Prot Group, Swiss Institute of Bioinformatics, CMU, 1 rue Michel Servet, CH-1211, Geneva 4, Switzerland., Sigrist CJA; Swiss-Prot Group, Swiss Institute of Bioinformatics, CMU, 1 rue Michel Servet, CH-1211, Geneva 4, Switzerland., Sillitoe I; Department of Structural and Molecular Biology, University College London, Gower St, Bloomsbury, London WC1E 6BT, UK., Thanki N; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA., Thomas PD; Division of Bioinformatics, Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90033, USA., Tosatto SCE; Department of Biomedical Sciences, University of Padua, via U. Bassi 58/b, 35131 Padua, Italy., Wu CH; Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USA.; Center for Bioinformatics and Computational Biology and Protein Information Resource, University of Delaware, Newark, DE 19711, USA., Bateman A; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.

Publikováno v: Nucleic acids research [Nucleic Acids Res] 2023 Jan 06; Vol. 51 (D1), pp. D418-D427.