Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains

Keywords

Biology, UniProt, Genome, Exploit, Computational biology

References

• Definition of general topological equivalence in protein structures. A procedure involving comparison of properties and relationships through simulated annealing and dynamic programming.Andrej Šali, Tom L. Blundell — 1990
• SUPERFAMILY: HMMs representing all proteins of known structure. SCOP sequence searches, alignments and genome assignmentsJulian Gough, C. Chothia — 2002
• Data growth and its impact on the SCOP database: new developmentsAntonina Andreeva, D. Howorth, J.-M. Chandonia — 2007
• Comparative Protein Structure Modeling Using ModellerNarayanan Eswar, Ben Webb, Marc A. Martı́-Renom — 2006
• CATHEDRAL: A Fast and Effective Algorithm to Predict Folds and Domain Boundaries from Multidomain Protein StructuresOliver Redfern, Andrew Harrison, Tim Dallman — 2007
• Protein structure alignment.William R. Taylor, Christine Orengo — 1989
• Statistical potential for assessment and prediction of protein structuresMin‐Yi Shen, Andrej Šali — 2006
• HOMSTRAD: A database of protein structure alignments for homologous familiesKenji Mizuguchi, Charlotte M. Deane, Tom L. Blundell — 1998
• FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties.Jiye Shi, Tom L. Blundell, Kenji Mizuguchi — 2001
• A graph‐theory algorithm for rapid protein side‐chain predictionAdrian A. Canutescu, Andrey Shelenkov, Roland L. Dunbrack — 2003
• A fast algorithm for the maximum clique problemPatric R. J. Östergård — 2002
• Gene3D: merging structure and function for a Thousand genomesJonathan Lees, Corin Yeats, Oliver Redfern — 2009
• Protein structure prediction on the Web: a case study using the Phyre serverLawrence A. Kelley, Michael J.E. Sternberg — 2009
• Comparative protein modelling by satisfaction of spatial restraints.Andrej Šali, Tom L. Blundell — 1993
• Cyclic coordinate descent: A robotics algorithm for protein loop closureAdrian A. Canutescu, Roland L. Dunbrack — 2003
• Methods of remote homology detection can be combined to increase coverage by 10% in the midnight zoneAdam J. Reid, Corin Yeats, Christine Orengo — 2007
• Extending CATH: increasing coverage of the protein structure universe and linking structure with functionAlison Cuff, I. Sillitoe, Ted G. Lewis — 2010
• Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure.Julian Gough, Kevin Karplus, Richard Hughey — 2001
• Characterization of pathogenic germline mutations in human Protein KinasesJosé M. G. Izarzugaza, Lisa Hopcroft, Anja Barešić — 2011
• The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB dataHelen M. Berman, K. Henrick, H. Nakamura — 2006

Cited by

• The integration of sequencing and bioinformatics in metagenomicsFirouz Abbasian, Robin Lockington, Mallavarapu Megharaj — 2015
• Integration and analysis of protein evolutionary relationships and small molecule bioactivity dataFelix A. Kruger — 2014
• The history of the CATH structural classification of protein domainsIan Sillitoe, Natalie L. Dawson, Janet M. Thornton — 2015
• The Phyre2 web portal for protein modelling, prediction and analysisLawrence A. Kelley, Stefans Mezulis, Christopher M. Yates — 2015
• New mini- zincin structures provide a minimal scaffold for members of this metallopeptidase superfamilyChristine B. Trame, Yuanyuan Chang, Herbert L. Axelrod — 2014
• Coiled-coil helix rotation selects repressing or activating state of transcriptional regulator DhaR.Rong Shi, Laura McDonald, Mirosław Cygler — 2014
• Classification of Intrinsically Disordered Regions and ProteinsRobin van der Lee, Marija Buljan, Benjamin Lang — 2014
• Open source libraries and frameworks for biological data visualisation: A guide for developersRui Wang, Yasset Pérez‐Riverol, Henning Hermjakob — 2015
• SuSPect: Enhanced Prediction of Single Amino Acid Variant (SAV) Phenotype Using Network FeaturesChristopher M. Yates, Ioannis Filippis, Lawrence A. Kelley — 2014
• A hybrid method for identification of structural domainsYongpan Hua, Min Zhu, Yuelong Wang — 2014
• Protein–protein interaction networks studies and importance of 3D structure knowledgeHui‐Chun Lu, Arianna Fornili, Franca Fraternali — 2013
• Cluster and Fold Stability of E. coli ISC-Type FerredoxinRobert Yan, Salvatore Adinolfi, Clara Iannuzzi — 2013
• Gene3D: Multi-domain annotations for protein sequence and comparative genome analysisJonathan Lees, David Lee, Romain A. Studer — 2013
• Genome3D: exploiting structure to help users understand their sequencesTony E. Lewis, Ian Sillitoe, Antonina Andreeva — 2014
• The plant RWP-RK transcription factors: key regulators of nitrogen responses and of gametophyte development.Camille Chardin, Thomas Girin, François Roudier — 2014
• The SUPERFAMILY 1.75 database in 2014: a doubling of dataMatt E. Oates, Jonathan Stahlhacke, Dimitrios V. Vavoulis — 2014
• Anatomy of BioJS, an open source community for the life sciencesGuy Yachdav, Tatyana Goldberg, Sebastian Wilzbach — 2015
• CHOPIN: a web resource for the structural and functional proteome of Mycobacterium tuberculosisBernardo Ochoa‐Montaño, Nishita Mohan, Tom L. Blundell — 2015
• The electrostatic profile of consecutive Cβ atoms applied to protein structure quality assessmentSandeep Chakraborty, Ravindra Venkatramani, Basuthkar J. Rao — 2013
• Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligentlyAndrew Currin, Neil Swainston, Philip J. Day — 2014

Related papers

• The success of structural genomicsThomas C. Terwilliger — 2011
• Structural Genomics and Nuclear Magnetic ResonanceDong Liu — 2001
• Solution NMR structure of protein HS00059 from Homo Sapiens. Northeast Structural Genomics Consortium (NESG) target HT98A.Alexander Lemak, Aleksandras Gutmanas, Christophe Farès — 2009
• Minimal Constraints Solution NMR Structure of Prospero Homeobox protein 1 from Homo sapiens. Northeast Structural Genomics Consortium Target HR4660B.P. Rossi, Lange, Oliver A., Hsiau‐Wei Lee — 2011
• Structural genomics is the largest contributor of novel structural leverageRajesh Nair, Jinfeng Liu, Ta-Tsen Soong — 2009
• Can Small Laboratories Do Structural GenomicsRonny C. Hughes, Joseph D. Ng — 2007
• A structural genomics initiative on yeast proteins.Sophie Quevillon‐Chéruel, Bruno Collinet, Cong‐Zhao Zhou — 2003
• Solution NMR Structure of CASP8-associated protein 2 from Homo sapiens, Northeast Structural Genomics Consortium (NESG) Target HR8150AS.V.S.R.K. Pulavarti, Bharathwaj Sathyamoorthy, A. Eletsky — 2012
• Structural genomics: opportunities and challenges.Peer R. E. Mittl, Markus G. Grütter — 2001
• From Structural Genomics to Functional GenomicsXinguo Li — 2006