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Tweets by ©PDBeurope f?1 Prntfain flata Rank Ro+u/faptfiH I Databases of Protein Folds SCOP (http://scop.berkeley.edu/) - known domain structure • Structural Classification of Proteins • Class-Fold-Superfamily-Family • Manual assembly by inspection Superfamily (http://supfam.org/SUPERFAMILY/) - predicted domain structures • HMM models for each SCOP fold • Fold assignments to all genome ORFs • Assessment of specificity/sensitivity of structure prediction • Search by sequence, genome and keywords CATH + Gene3D (http://www.biochem.ucl.ac.uk/bsm/cath/) - both • Class - Architecture - Topology - Homologous Superfamily • Manual classification at Architecture level • Automated topology classification using SSAP (Orengo & Taylor) PDB eFold (http://www.ebi.ac.uk/msd-srv/ssm/) • Fully automated using the DALI algorithm (Holm & Sander) Pfam (http://pfam.xfam.org)- domain sequences (MSA, HMM) SCOP Structural Classification of Proteins (http://scop.mrc-lmb.cam.ac.uk/scop) ;55 9 • Welcome to SCOP: Structural Classification of Proteins. 1.75 release (June 2009) 38221 PDB Entries. 1 Literature Reference. 110S00 Domains, (excluding nucleic acids and theoretical models). Folds: superfamilies, and families statistics here-New folds superfamilies families. List of obsolete entries and their replacements. Authors. Alexey G. Murzin, John-Marc Chandonia, Antonina Andreeva, Dave Ho\vorth: Loredana Lo Conte: Bartlett G. Ailey, Steven E. Brenner Tim J. P. Hubbard, and Cyrus Chothia. scopffmrc-lmb.cam.ac.uk Reference: Murzm A. G.: Brenner S. E., Hubbard T.: Chothia C. (1995). SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247, 536-540. fPDFI Recent changes are described in: Lo Conte L., Brenner S. E.: Hubbard T.J.P., Chothia C, Murzm A. (2002). SCOP database in 2002: refinements accommodate structural genomics. Xucl. Acid Res. 30(1), 264-267. [PDF], Andreeva A., Howorth D., Brenner S.E., Hubbard T.J.P., Chothia C, Murzm AG. (2004). SCOP database in 2004: refinements integrate structure and sequence family data. Xucl. Acid Res. 32:D226-D229. [PDF], and Andreeva A., Howorth D., Chandonia J.-M., Brenner S.E.: Hubbard T.J.P.: Chothia C, Murzin A.G. (2007). Data growth and its impact on the SCOP database: new developments. Xucl. Acid Res, advance access, doi:10.1093 nar gkm993. [PDF]. Access methods Enter SCOP at the top of the hierarchy Kevword search of SCOP entries SCOP parseable files (MRC site) All SCOP releases and reclassified entry history (MRC site) pi e-SCOP - preview of the next release SCOP domain sequences and pdb-style coordinate files (ASTRAL) 11>I -ra-T»T- A \ rrr v\ The SCOP database, created by manual inspection and abetted by a battery of automated methods, aims to provide a detailed and comprehensive description of the structural and evolutionary relationships between all proteins whose structure is known, http://scop.mrc-lmb.cam.ac.uk/scop Family: Clear evolutionorily relationship Proteins clustered together into families are clearly evolutionarily related. Generally, this means that pairwise residue identities between the proteins are 30% and greater. However, in some cases similar functions and structures provide definitive evidence of common descent in the absense of high sequence identity; for example, many globinsform a family though some members have sequence identities of only 15%. Superfamily: Probable common evolutionary origin Proteins that have low sequence identities, but whose structural and functional features suggest that a common evolutionary origin is probable are placed together in SUperfamilies. For example, actin, theATPase domain of the heat shock protein, and hexa kinase together form a superfamily. Fold: Major structural similarity Proteins are defined as having a common fold if they have the same major secondary structures in the same arrangement and with the same topological connections. Different proteins with the same fold often have peripheral elements of secondary structure and turn regions that differ in size and conformation. Proteins placed together in the same fold category may not have a common evolutionary origin: the structural similarities could arise just from the physics and chemistry of proteins favoring certain packing arrangements and chain topologies. SCOP: Root scop - Mozilla Firefox Soubor Úpravy Zobrazit Historie Záložky Nástroje Nápověda w C ^ ( & I http://scop.mrc-lmb.cam.ac.Uk/scop/data/scop.b.html fi Nejnavštévovanéjší Jak začřt Přehled zpráv % http://www.ncbi.nlm.... G005 http://www.grycoscie... - CHMI Radar Departme.. ]|£|| / TL Root: scop Classes: 1. AH alpha pr [46456] (258) 1 2. Afl beta proteins [48724] (165) 1 3. Alpha and beta proteins Cab) T513491 (141) 1 Mainly parallel beta sheets (beta-alpha-beta units) 4. Alpha and beta proteins (a-b) [539311 (334) 1 Mainly antiparallel beta sheets (segregated alpha and beta regions) 5. Multi-domain proteins (alpha and beta) [565721 (53) Folds consisting of two or more domains belonging to different classes 6. Membrane and cell surface proteins and peptides [568351 (50) MS Does not include proteins in the immune system 7. Small proteins [56992] (85) 1 Usually dominated by metal ligand, heme, and!or disulfide bridges 8. Coiled coil proteins [579421 (7) 1 Not a true class . Low resolution protein structures [58117] (26) Kl Not a true class .0. Peptides [582311 (120)1 Peptides and fragments. Not a true class 11. Designed proteins [587881 (44)1 Experimental structures of proteins with essentially non-natural sequences. Not a true class search ke\ Search _ _ Laboratory of KL Molecular Biology Structural Classification of Proteins 2 About Browser News November,2013 During the development of SCOP2, we have identified a new, previously unrecognised type of alpha-alpha superhelix. Unlike other alpha-alpha superhelices.. More... January, 2014 SCOP2 article in NAR is published More... January, 2014 The structure of the month More... Welcome to SCOP2! Citation Antonína Andreeva, Dave Howorth, Cyrus Chothia, Eugene Kulesha, Alexey Murzin, SCOP2 prototype: a new approach to protein structure mining (2014) Nucl. Acid Res., 42 (Dl): D310-D314. [PDF] Description of the SCOP2 database SCOP2 is a successor of Structural classification of proteins (SCOP). Similarly to SCOP, the main focus of SCOP2 is on proteins that are structurally characterized and deposited in the PDB. Proteins are organized according to their structural and evolutionary relationships, but, in contrast to SCOP, instead of a simple tree-like hierarchy these relationships form a complex network of nodes. Each node represents a relationship of a particular type and is exemplified by a region of protein structure and sequence. In SCOP2, we try to put in use the knowledge we acquired over the past years and the lessons we have learned during the classification of protein structures. We believe that there are many peculiarities of proteins and their structures that have been missed due to the constraints of the original SCOP hierarchical schema. We hope that our users will find the new resource useful and that it could open new avenues for protein analysis and research. Search Browser Search Add an asterisk to search free text (e.g. serine*) Search Graph Search Add an asterisk to search free text (e.g. protein*domain) Quick introduction on how to browse, search and download SCOP2 offers two different ways for accessing data: SCOP2-browser, that allows navigation through the SCOP2 classification in a traditional way by browsing pages displaying the node information, and SCOP2-graph, which is a graph-based web tool for Hicnlav anH navinarinn rhrnnnh rhp yriP7 Haccifirarinn_Rnrh rnnk nrnwiHp cparrh nf ™*"-02 © 2014 MRC Laboratory of Molecular Biology Display a menu http://scop2.mrc-lmb.cam.ac.uk/front.html SCOPe Browse Stats & History Downloads - Help - Search SCOPe Welcome to SCOPe! SCOPe (Structural Classification of Proteins — extended) is a database developed at the Berkeley Lab and UC Berkeley to extend the development and maintenance of SCOP. SCOP was conceived at the MRC Laboratory of Molecular Biology, and developed in collaboration with researchers in Berkeley. Work on SCOP (version 1) concluded in June 2009 with the release of SCOP 1.75. SCOPe classifies many newer structures through a combination of automation and manual curation, and corrects some errors in SCOP, aiming to have the same accuracy as the hand-curated SCOP releases. SCOPe also incorporates and updates the Astral database. About SCOPe I Stats & Prior Releases Click for information about changes to SCOP(e) design and size. News 2019-04-11: New pdb entries were added in a periodic update; for more info on these updates, see the online documentation. 2019-03-05: We added an additional archive of PDB-style coordinate files for domains that were inadvertently omitted from our coordinate file archives. 2018-11-30: We published a paper describing updates to SCOPe, focusing on our findings from classifying large structres. [PDF]. 2018-03-02: SCOPe 2.07-stable has been released, with nearly 10,000 new pdb entries added since the last stable release. Click either the About or Stats & History links for more details on what's new! Rtwitro*3uCboo of rrttrtuMp improved iulOffiWdc*—»OcMKft MM man**