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The PSI KB Protein Model Portal Torsten Schwede NIGMS PSI „Bottlenecks“ Workshop Bethesda, April 14, 2008 Swiss Institute of Bioinformatics.

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Presentation on theme: "The PSI KB Protein Model Portal Torsten Schwede NIGMS PSI „Bottlenecks“ Workshop Bethesda, April 14, 2008 Swiss Institute of Bioinformatics."— Presentation transcript:

1 The PSI KB Protein Model Portal Torsten Schwede NIGMS PSI „Bottlenecks“ Workshop Bethesda, April 14, 2008 Swiss Institute of Bioinformatics

2 Overview: The KB Modeling Portal Introduction The KB Protein Model Portal Mission and Goals Version 1.0: Content, Features & Technical Implementation Outlook: Next steps New Features & Functions Modeling Portal Community Workshop Questions & Discussion

3

4 gggtctctcttgttagaccagatctgagcctgggagctctctggctaactagggaacccactgcttaagcctcaataaagcttgccttgagtgcttcaagtagtgtgtgcccgtctgttgtgtgactctgatagctagagatcccttc agaccaaatttagtcagtgtgaaaaatctctagcagtggcgcctgaacagggacttgaaagcgaaagagaaaccagagaagctctctcgacgcaggactcggcttgctgaagcgcgcacggcaagaggcgaggggacggcgactggtg agtacgccaaaattttgactagcggaggctagaaggagagagatgggtgcgagagcgtcgatattaagcgggggaggattagatagatgggaaaaaattcggttaaggccagggggaaagaaaaaatatagattaaaacatttagtat gggcaagcagggagctagaacgattcgcagtcaatcctggcctattagaaacatcagaaggttgtagacaaatactgggacaactacaaccagcccttcagacaggatcagaagaacttagatcattatataatacagtagcaaccct ctattgtgtgcatcaaaagatagatgtaaaagacaccaaggaagctttagataagatagaggaagagcaaaacaaaagtaagaaaaaagcacagcaagcagcagctgacacaggaaatagcagccaggtcagccaaaattaccccata gtgcagaacatccaggggcaaatggtacatcaggccatatcacctagaactttaaatgcatgggtaaaagtagtagaagagaaggctttcagcccagaagtaatacccatgttttcagcattatcagaaggagccaccccacaagatt taaacaccatgctaaacacagtggggggacatcaagcagccatgcaaatgttaaaagagaccatcaatgaggaagctgcagaatgggatagattgcatccagtgcatgcagggcctcatccaccaggccagatgagagaaccaagggg aagtgacatagcaggaactactagtacccttcaggaacaaatagcatggatgacaaataatccacctatcccagtaggagaaatctataagagatggataatcctgggattaaataaaatagtaaggatgtatagccctaccagcatt ctggacataaaacaaggaccaaaggaaccctttagagactatgtagaccggttctataagactctaagagccgagcaagcttcacaggaggtaaaaaattggatgacagaaaccttgttggtccaaaatgcgaacccagattgtaaga ctattttaaaagcattgggaccagcagctacactagaagaaatgatgacagcatgtcagggagtgggaggacccggccataaagcaagagttttggcagaagcaatgagccaagtaacaaattcagctaccataatgatgcagaaagg caattttaggaaccaaagaaaaattgttaagtgtttcaattgtggcaaagaagggcacatagccaaaaattgcagggcccctaggaaaaggggctgttggaaatgtggaaaggagggacaccaaatgaaagattgtactgagagacag gctaattttttagggaaaatctggccttcccacaggggaaggccagggaattttcctcagaacagactagagccaacagccccaccagccccaccagaagagagcttcaggtttggggaagagacaacaactccctctcagaagcagg agctgatagacaaggaactgtatccttcagcttccctcaaatcactctttggcaacgaccccttgtcacaataaagataggggggcaactaaaggaagctctattagatacaggagcagatgatacagtattagaagaaataaatttg ccaggaagatggaaaccaaaaatgatagggggaattggaggttttatcaaagtaagacagtatgatcaaatactcgtagaaatctgtggacataaagctataggtacagtattagtaggacctacacctgtcaacataattggaagaa atctgttgactcagattggttgcactttaaattttcccattagtcctattgaaactgtaccagtaaaattaaagccaggaatggatggcccaaaagttaaacaatggccattgacagaagaaaaaataaaagcattagtagaaatctg tacagaaatggaaaaggaaggaaaaatttcaaaaatcgggcctgaaaatccatataatactccagtatttgccataaagaaaaaagacagtactaaatggagaaaattagtagatttcagagaacttaataagaaaactcaagacttc tgggaagttcaattaggaataccacatcccgcagggttaaaaaagaaaaaatcagtaacagtactggatgtgggtgatgcatatttttcagttcccttagataaagaattcaggaagtacactgcatttaccatacctagtataaaca atgagacaccagggattagatatcagtacaatgtgcttccacagggatggaaaggatcaccagcaatattccaaagcagcatgacaaaaatcttagagccttttagaaaacaaaatccagacatagttatctatcaatacatggacga tttgtatgtaggatctgacttagaaatagggcagcatagaacaaaaatagaggaactgagacaacatctgttgaagtggggatttaccacaccagacaaaaaacatcagaaagaacctccattcctttggatgggttatgaactccat cctgataaatggacagtacagcctatagtgctgccagaaaaggacagctggactgtcaatgacatacagaagttagtgggaaaattgaattgggcaagtcagatttacccagggattaaagtaaagcaattatgtagactccttaggg gaaccaaggcactaacagaagtaataccactaacaaaagaagcagagctagaactggcagaaaacagggaaattctaaaagaaccagtacatggagtgtattatgacccatcaaaagacttaatagcggaaatacagaagcaggggca aggtcaatggacatatcaaatttatcaagagccatttaaaaatctgaaaacaggaaaatatgcaagaatgaggggtgcccacactaatgatgtaaaacaattaacagaggcagtgcaaaaaataaccacagaaagcatagtaatatgg ggaaagactcctaaatttaaactacccatacaaaaagaaacatgggaaacatggtggacagagtattggcaagccacctggattcctgagtgggagtttgtcaatacccctcccttagtaaaattatggtaccagttagagaaagaac ccataataggagcagaaactttctatgtagatggggcagctaacagggagactaaattaggaaaagcaggatatgttactaacaaagggagacaaaaagttgtctccataactgacacaacaaatcagaagactgagttacaagcaat tcttctagcattacaggattctggattagaagtaaacatagtaacagactcacaatatgcattaggaatcattcaagcacaaccagataaaagtgaatcagagatagtcagtcaaataatagagcagttaataaaaaaagaaaaggtc tacctgacatgggtaccagcgcacaaaggaattggaggaaatgaacaagtagataaattagtcagtactggaatcaggaaagtactctttttagatggaatagataaagcccaagaagaacatgaaaaatatcacagtaattggaggg caatggctagtgattttaacctgccacctgtggtagcaaaagagatagtagccagctgtgataaatgtcagctaaaaggagaagccatgcatggacaagtagactgtagtccaggaatatggcaactagattgtacacatttagaagg aaaaattatcctggtagcagttcatgtagccagtggatatatagaagcagaagttattccagcagaaacagggcaggaaacagcatactttctcttaaaattagcaggaagatggccagtaaaaacagtacatacagacaatggcagc aatttcaccagtactacagttaaggccgcctgttggtgggcaggaatcaagcaggaatttggcattccctacaatccccaaagtcaaggagtagtagaatctataaataaagaattaaagaaagttataggacagataagagatcagg ctgaacatcttaagacagcagtacaaatggcagtattcatccacaattttaaaagaaaaggggggattggggggtacagtgcaggggaaagaatagtagacataatagcaacagacatacaaactaaagaactacaaaaacaaattac 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tcatttcagaattgggtgtcaacatagcagaatagacattcttcgacgaaggagagcaagaaatggagccagtagatcctagactagagccctggaagcatccaggaagtcagcctaggactgcttgtaccaattgctattgtaaaaa gtgttgctttcattgccaagtttgtttcataacaaaaggcttaggcatctcctatggcaggaagaagcggagacagcgacgaagagctcctcaagacagtcagactcatcaagtttctctatcaaagcagtaagtagtacatgtaatg caatctttacaaatattagcagtagtagcattagtagtagcagcaataatagcaatagttgtgtggtccatagtattcatagaatataggaaaataagaagacaaaacaaaatagaaaggttgattgatagaataatagaaagagcag aagacagtggcaatgagagtgacggagatcaggaagaattatcagcacttgtggaaatggggcacgatgctccttgggatgttaatgatctgtaaagctgcagaaaatttgtgggtcacagtttattatggggtacctgtgtggaaag aagcaaccaccactctattttgtgcctcagatgctaaagcgtatgatacagaggtacataatgtttgggccacacatgcctgtgtacccacagaccccaacccacaagaagtagaactgaagaatgtgacagaaaattttaacatgtg gaaaaataacatggtagaccaaatgcatgaggatataattagtttatgggatcaaagcctaaagccatgtgtaaaattaaccccactctgtgttactttaaattgcactgattatgggaatgatactaacaccaataatagtagtgct actaaccccactagtagtagcgggggaatggaggggagaggagaaataaaaaattgctctttcaatatcaccagaagcataagagataaagtgaagaaagaatatgcacttttttatagtcttgatgtaataccaataaaagatgata atactagctataggttgagaagttgtaacacctcagtcattacacaggcctgtccaaaggtatcctttgaaccaattcccatacattattgtgccccggctggttttgcgattctaaagtgtaatgataaaaagttcaatggaaaagg accatgtacaaatgtcagcacagtacaatgtacacatggaattaggccagtagtatcaactcaactgctgttaaatggcagtctagcagaagaagaggtagtaattagatcagacaatttctcggacaatgctaaagtcataatagta catctgaatgaatctgtagaaattaattgtacaagactcaacaacattacaaggagaagtatacatgtaggacatgtaggaccaggcagagcaatttatacaacaggaataataggaaaaataagacaagcacattgtaacattagta gagcaaaatggaataacactttaaaacagatagttacaaaattaagagaacaatttaagaataaaacaatagtctttaatcaatcctcaggaggggacccagaaattgtaatgcacagttttaattgtggaggggaatttttctactg taattcaacacaactgtttaacagtacttggaatggtactgcatggtcaaataacactgaaggaaatgaaaatgacacaatcacactcccatgcagaataaaacaaattataaacatgtggcaggaagtaggaaaagcaatgtatgca cctcccatcagaggacaaattagatgttcatcaaatattacagggctgatattaacaagagatggtggtattaaccagaccaacaccaccgagattttcaggcctggaggaggagatatgaaggacaattggagaagtgaattatata aatataaagtagtaaaaattgaaccattaggagtagcacccaccaaggcaaagagaagagtggtgcaaagagaaaaaagagcagtgggaataataggagctatgctccttgggttcttgggagcagcaggaagcactatgggcgcagc gtcaatgacgctgacggtacaggccagacaattattgtctggtatagtgcaacagcagaacaatttgctgagggctattgaggcgcaacagcatctgttgcacctcacagtctggggcatcaagcagctccaagcaagagtcctggct gtggaaagatacctaagggatcaacagctcctggggttttggggttgctctggaaaactcatttgcaccactgctgtgccttggaatactagttggagtaataaatctctgagtcagatttgggataacatgacctggatgcagtggg aaagggaaattgataattacacaagcttaatatacaacttaattgaagaatcgcaaaaccaacaagaaaagaatgaacaagagttattggaattagataactgggcaagtttgtggaattggtttagcataacaaattggctgtggta tataaaaatattcataatgatagtaggaggcttggtaggtttaagaatagtttttactgtactttctatagtaaatagagttaggcagggatactcaccattgtcgtttcagacgcgcctcccagccaggaggggacccgacaggccc gaaggaatcgaagaagaaggtggagagagagacagagacagatccggtcaattagtggatggattcttagcaattatctgggtcgacctgcggagcctgtgcctcttcagctaccaccgcttgagagacttactcttgattgtaacga ggattgtggaacttctgggacgcagggggtgggaagccctcaaatattggtggaatctcctacaatattggattcaggaactaaagaatagtgctgttagcttgctcaacgccacagccatagcagtagctgagggaactgatagggt

5 Public Database Content (Sources: PDB, EBI, SIB)

6 How can we find out if there is a model available for a given protein sequence? Well Overview: The KB Modeling Portal

7 The goal of the KB Protein Model Portal is to give access to the all models that can be leveraged from PSI targets and other experimental protein structures. The Protein Model Portal aims to provide a single interface to query simultaneously the existing pre-computed models at various sites, gives access to interactive services for template selection, target-template alignment, model building, and quality assessment. The KB Protein Model Portal

8 The KB Protein Model Portal does NOT: build models or develop modeling methods, but provides an interface to the participating expert groups and services; store all models in a database, but provides a query interface to the models provided by the partner sites; judge the quality of the models provided, but provides an interface to services for structure comparison and evaluation; The KB Protein Model Portal

9 How can we organize protein model data from different sources in a single portal? Data view of the PDB is „experiment centric“, i.e. unique PDB IDs are assigned to structures that result from of a specific experiment. Data view of models is “sequence centric”, i.e. one or more models are build for a segment of a specific protein sequence (“target”) based on one or more experimental structures (“templates”). Typical example: Target Sequence Models

10 Bottlenecks: There is no common registry scheme for protein models. For each target protein sequence, an ensemble of models will be available based on different templates, alternative alignments, and modeling methods. Models will generally cover only fractions of the target sequence; parts of the target sequence might be missing, e.g. non modeled loops. Protein models must update frequently to reflect updates of target sequence databases (UniProt), template structure databases (PDB), and algorithmic improvements. The KB Protein Model Portal

11 Bottlenecks: Sequence database accession codes are neither unique, nor stable. Some groups do not store pre-computed models, but calculate models “on the fly”. Some models will be based on outdated target sequences.  Target protein sequences will be uniquely identified by hash values (UTSI) of their full length sequences as reference space. The KB Protein Model Portal

12 Data mapping of target sequences and structure models Unique (full length) target protein sequences are used as reference space to group models for identical targets. Target protein sequences will be uniquely identified by Hash function values (UTSI). >P68399|CSK21_BOVIN Casein kinase II subunit alpha - Bos taurus MSGPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINIT NNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTD FKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAE FYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYD QLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDF LDKLLRYDHQSRLTAREAMEHPYFYTVVKDQARMGSSSMPGGSTPVSSANMMSGISSVPT PSPLGPLAGSPVIAAANPLGMPVPAAAGAQQ >P68400|CSK21_HUMAN Casein kinase II subunit alpha - Homo sapiens MSGPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINIT NNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTD FKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAE FYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYD QLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDF LDKLLRYDHQSRLTAREAMEHPYFYTVVKDQARMGSSSMPGGSTPVSSANMMSGISSVPT PSPLGPLAGSPVIAAANPLGMPVPAAAGAQQ >Q5U065|Q5U065_HUMAN Casein kinase 2, alpha 1 polypeptide - Homo sapiens MSGPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINIT NNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTD FKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAE FYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYD QLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDF LDKLLRYDHQSRLTAREAMEHPYFYTVVKDQARMGSSSMPGGSTPVSSANMMSGISSVPT PSPLGPLAGSPVIAAANPLGMPVPAAAGAQQ >Q9D9I4|TBC20_MOUSE TBC1 domain family member 20 - Mus musculus MALRPSKGDGSAGRWDRGAGKADFNAKRKKKVAEIHQALNSDPIDLAALRRMAISEGGLL TDEIRCQVWPKLLNVNTSEPPPVSRKDLRDMSKDYQQVLLDVRRSLRRFPPGMPDEQREG LQEELIDIILLVLDRNPQLHYYQGYHDIVVTFLLVVGERLATSLVEKLSTHHLRDFMDPT MDNTKHILNYLMPIIDQVSPELHDFMQSAEVGTIFALSWLITWFGHVLMDFRHVVRLYDF FLACHPLMPIYFAAVIVLYREQEVLDCDCDMASVHHLLSQIPQDLPYETLISRAGDLFVQ FPPSELAREAAAQQEAERTAASTFKDFELASTQQRPDMVLRQRFRGLLRPEARTKDVLTK PRTNRFVKLAVMGLTVALGAAALAVVKSALEWAPKFQLQLFP >ipi|IPI |IPI CASEIN KINASE II SUBUNIT ALPHA. MSGPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINIT NNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTD FKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAE FYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYD QLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDF LDKLLRYDHQSRLTAREAMEHPYFYTVVKDQARMGSSSMPGGSTPVSSANMMSGISSVPT PSPLGPLAGSPVIAAANPLGMPVPAAAGAQQ CRC64:D3B6F5D13FF7422D MD5:b6f2c321d42d50b b5166 UPI:UPI CB5 CRC64:A3B6F5D13DF7422E MD5:605f4802e88ec1443d36520ac05df3b9 UPI:UPI DatabaseEntryVersionOrganismFirst SeenLast SeenActive UniProtKB/Swiss-ProtP683991Bos taurus (Bovine) Yes UniProtKB/Swiss-ProtP684001Homo sapiens (Human) Yes UniProtKB/Swiss-ProtP No UniProtKB/TrEMBLQ5U0651Homo sapiens (Human) Yes TrEMBLnewAAH No TrEMBLnewAAH No International Protein Index (IPI)IPI No International Protein Index (IPI)IPI Homo sapiens (Human) Yes International Protein Index (IPI)IPI Bos taurus (Bovine) Yes RefSeqNP_ Yes RefSeqNP_ No RefSeqNP_ No RefSeqXP_ Yes RefSeqXP_ Yes RefSeqXP_ Yes EnsemblENSCAFP Canis familiaris (Dog) Yes EnsemblENSP Homo sapiens (Human) Yes EnsemblENSP Homo sapiens (Human) Yes EnsemblENSP No EnsemblENSMMUP Macaca mulatta (Rhesus macaque) Yes EMBL Annotated CONsEAX106651Homo sapiens (Human) Yes EMBL CDSAAA355031Homo sapiens (Human) Yes PIR-PSD ArchiveA Yes European Patent Office (EPO)CS Yes US Patent Office (USPO)AAE Yes Japan Patent Office (JPO)BD Yes TROMENT_011387_19_ No H-Invitational Database (H-InvDB)HIT Homo sapiens (Human) No Real time annotation The KB Protein Model Portal

13 Module 3 Protein Model Portal GUI PSI SGKB Portal www SOAP wsdl Metadata unification, access code mapping, generation of data warehouse and search indices Module 3 Protein Model Portal (PMP) Backend queries SQL TCP/IP socket LRMS (SGE) model meta database (mySQL) model sequence similarity queries (Blast) SGE Linux Cluster model target sequence match server (C/C++) Link to coordinate s at model provider REST The KB Protein Model Portal

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17 The KB Protein Model Portal

18 UniProt ( REST query uniprot.org) InterPro (Pfam) (DAS query) Model Preview Image (generated on the fly with coordinates from provider; REST) Model Meta Information (PMP model meta information DB, SOAP) Target Template Alignment (structural alignment with template; generated on the fly; REST) Model Download (link to original structure provider) The KB Protein Model Portal

19 Overview: The KB Model Portal Introduction Protein Model Portal Mission and Goals PMP Version 1.0: Content and Features Technical Implementation Outlook: Next steps New Features & Functions Modeling Portal Community Workshop Questions & Discussion

20 Outlook: Next steps New Features & Functions Better visualization of query results

21 Outlook: Next steps New Features & Functions Better visualization of query results Interactive structure / model comparison Visualization of mapped properties (sequence conservation; quality assessment results; UniProt annotation) Residue-level annotations (UniProt, InterPro) Model quality assessment tools

22 Accuracy and application of protein structure models Baker D, Sali A. Protein structure prediction and structural genomics. (2001) Science. 294:93-96.

23 Community Workshop Workshop on Applications of Protein Models in Biomedical Research University of California, San Francisco July 11 &12, 2008 How are protein structure models used in biomedical research projects today? Which requirements and limitations exist for the different applications? Structure based drug design Analysis of SNPs and disease related mutations Phasing X-ray crystallography data by molecular replacement Interpretation of low-resolution experimental data Protein engineering and design Functional characterization of novel proteins

24 Community Workshop Workshop on Applications of Protein Models in Biomedical Research University of California, San Francisco July 11 &12, 2008 We need your input! Please... participate in the workshop; send us examples of successful use of models in your work, and negative examples when models did not do what you expected; let us know, what you expect from proteins models, and which aspects of modeling techniques need improvement to make models more useful to your research.

25 Acknowledgements Biozentrum & SIB, University of Basel Michael Podvinec Jürgen Kopp Lorenza Bordoli Rainer Pöhlmann Konstantin Arnold James Battey Pascal Benkert Florian Kiefer SIB Geneva Eric Jain Funding: NIH – National Institutes of Health SIB – Swiss Institue of Bioinformatics RCSB-PDB Helen Berman John Westbrook Wendy Tao FCCC/NMHRCM Roland Dunbrack Jr. UCSF/NYSGXRC Andrej Sali Ursula Pieper MCSG Christine Orengo David Lee JCMM Adam Godzik NESG Diana Murray


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