1 / 25

The PSI KB Protein Model Portal

The PSI KB Protein Model Portal. Torsten Schwede NIGMS PSI „Bottlenecks“ Workshop Bethesda, April 14, 2008. Swiss Institute of Bioinformatics. Overview: The KB Modeling Portal. Introduction The KB Protein Model Portal Mission and Goals

diza
Download Presentation

The PSI KB Protein Model Portal

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

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. gggtctctcttgttagaccagatctgagcctgggagctctctggctaactagggaacccactgcttaagcctcaataaagcttgccttgagtgcttcaagtagtgtgtgcccgtctgttgtgtgactctgatagctagagatcccttcagaccaaatttagtcagtgtgaaaaatctctagcagtggcgcctgaacagggacttgaaagcgaaagagaaaccagagaagctctctcgacgcaggactcggcttgctgaagcgcgcacggcaagaggcgaggggacggcgactggtgagtacgccaaaattttgactagcggaggctagaaggagagagatgggtgcgagagcgtcgatattaagcgggggaggattagatagatgggaaaaaattcggttaaggccagggggaaagaaaaaatatagattaaaacatttagtatgggcaagcagggagctagaacgattcgcagtcaatcctggcctattagaaacatcagaaggttgtagacaaatactgggacaactacaaccagcccttcagacaggatcagaagaacttagatcattatataatacagtagcaaccctctattgtgtgcatcaaaagatagatgtaaaagacaccaaggaagctttagataagatagaggaagagcaaaacaaaagtaagaaaaaagcacagcaagcagcagctgacacaggaaatagcagccaggtcagccaaaattaccccatagtgcagaacatccaggggcaaatggtacatcaggccatatcacctagaactttaaatgcatgggtaaaagtagtagaagagaaggctttcagcccagaagtaatacccatgttttcagcattatcagaaggagccaccccacaagatttaaacaccatgctaaacacagtggggggacatcaagcagccatgcaaatgttaaaagagaccatcaatgaggaagctgcagaatgggatagattgcatccagtgcatgcagggcctcatccaccaggccagatgagagaaccaaggggaagtgacatagcaggaactactagtacccttcaggaacaaatagcatggatgacaaataatccacctatcccagtaggagaaatctataagagatggataatcctgggattaaataaaatagtaaggatgtatagccctaccagcattctggacataaaacaaggaccaaaggaaccctttagagactatgtagaccggttctataagactctaagagccgagcaagcttcacaggaggtaaaaaattggatgacagaaaccttgttggtccaaaatgcgaacccagattgtaagactattttaaaagcattgggaccagcagctacactagaagaaatgatgacagcatgtcagggagtgggaggacccggccataaagcaagagttttggcagaagcaatgagccaagtaacaaattcagctaccataatgatgcagaaaggcaattttaggaaccaaagaaaaattgttaagtgtttcaattgtggcaaagaagggcacatagccaaaaattgcagggcccctaggaaaaggggctgttggaaatgtggaaaggagggacaccaaatgaaagattgtactgagagacaggctaattttttagggaaaatctggccttcccacaggggaaggccagggaattttcctcagaacagactagagccaacagccccaccagccccaccagaagagagcttcaggtttggggaagagacaacaactccctctcagaagcaggagctgatagacaaggaactgtatccttcagcttccctcaaatcactctttggcaacgaccccttgtcacaataaagataggggggcaactaaaggaagctctattagatacaggagcagatgatacagtattagaagaaataaatttgccaggaagatggaaaccaaaaatgatagggggaattggaggttttatcaaagtaagacagtatgatcaaatactcgtagaaatctgtggacataaagctataggtacagtattagtaggacctacacctgtcaacataattggaagaaatctgttgactcagattggttgcactttaaattttcccattagtcctattgaaactgtaccagtaaaattaaagccaggaatggatggcccaaaagttaaacaatggccattgacagaagaaaaaataaaagcattagtagaaatctgtacagaaatggaaaaggaaggaaaaatttcaaaaatcgggcctgaaaatccatataatactccagtatttgccataaagaaaaaagacagtactaaatggagaaaattagtagatttcagagaacttaataagaaaactcaagacttctgggaagttcaattaggaataccacatcccgcagggttaaaaaagaaaaaatcagtaacagtactggatgtgggtgatgcatatttttcagttcccttagataaagaattcaggaagtacactgcatttaccatacctagtataaacaatgagacaccagggattagatatcagtacaatgtgcttccacagggatggaaaggatcaccagcaatattccaaagcagcatgacaaaaatcttagagccttttagaaaacaaaatccagacatagttatctatcaatacatggacgatttgtatgtaggatctgacttagaaatagggcagcatagaacaaaaatagaggaactgagacaacatctgttgaagtggggatttaccacaccagacaaaaaacatcagaaagaacctccattcctttggatgggttatgaactccatcctgataaatggacagtacagcctatagtgctgccagaaaaggacagctggactgtcaatgacatacagaagttagtgggaaaattgaattgggcaagtcagatttacccagggattaaagtaaagcaattatgtagactccttaggggaaccaaggcactaacagaagtaataccactaacaaaagaagcagagctagaactggcagaaaacagggaaattctaaaagaaccagtacatggagtgtattatgacccatcaaaagacttaatagcggaaatacagaagcaggggcaaggtcaatggacatatcaaatttatcaagagccatttaaaaatctgaaaacaggaaaatatgcaagaatgaggggtgcccacactaatgatgtaaaacaattaacagaggcagtgcaaaaaataaccacagaaagcatagtaatatggggaaagactcctaaatttaaactacccatacaaaaagaaacatgggaaacatggtggacagagtattggcaagccacctggattcctgagtgggagtttgtcaatacccctcccttagtaaaattatggtaccagttagagaaagaacccataataggagcagaaactttctatgtagatggggcagctaacagggagactaaattaggaaaagcaggatatgttactaacaaagggagacaaaaagttgtctccataactgacacaacaaatcagaagactgagttacaagcaattcttctagcattacaggattctggattagaagtaaacatagtaacagactcacaatatgcattaggaatcattcaagcacaaccagataaaagtgaatcagagatagtcagtcaaataatagagcagttaataaaaaaagaaaaggtctacctgacatgggtaccagcgcacaaaggaattggaggaaatgaacaagtagataaattagtcagtactggaatcaggaaagtactctttttagatggaatagataaagcccaagaagaacatgaaaaatatcacagtaattggagggcaatggctagtgattttaacctgccacctgtggtagcaaaagagatagtagccagctgtgataaatgtcagctaaaaggagaagccatgcatggacaagtagactgtagtccaggaatatggcaactagattgtacacatttagaaggaaaaattatcctggtagcagttcatgtagccagtggatatatagaagcagaagttattccagcagaaacagggcaggaaacagcatactttctcttaaaattagcaggaagatggccagtaaaaacagtacatacagacaatggcagcaatttcaccagtactacagttaaggccgcctgttggtgggcaggaatcaagcaggaatttggcattccctacaatccccaaagtcaaggagtagtagaatctataaataaagaattaaagaaagttataggacagataagagatcaggctgaacatcttaagacagcagtacaaatggcagtattcatccacaattttaaaagaaaaggggggattggggggtacagtgcaggggaaagaatagtagacataatagcaacagacatacaaactaaagaactacaaaaacaaattacaaaaattcaaaattttcgggtttattacagggacagcagagatccactttggaaaggaccagcaaagcttctctggaaaggtgaaggggcagtagtaatacaagataatagtgacataaaagtagtgccaagaagaaaagcaaagatcattagggattatggaaaacagatggcaggtgatgattgtgtggcaagtagacaggatgaggattagaacatggaaaagtttagtaaaacaccatatgtatgtttcaaggaaagctaagggatggttttatagacatcactatgaaagtactcatccgagaataagttcagaagtacacatcccactagggaatgcaaaattggtaataacaacatattggggtctacatacaggagaaagagactggcatttgggtcaaggagtctccatagaattgaggaaaaggagatatagcacacaattagaccctaacctagcagaccaactaattcatctgcattactttgattgtttttcagaatctgctataagaaatgccatattaggacatatagttagccctaggtgtgaatatcaagcaggacataacaaggtaggatctctacagtacttggcactaacagcattagtaagaccaagaaaaaagataaagccacctttgcctagtgttacaaaactgacagaggatagatggaacaagccccagaagaccaagggccacaaagggaaccatacaatgaatggacactagaacttttagaggagctcaagaatgaagctgttagacattttcctaggatatggctccatagcttagggcaacatatctatgaaacttatggagatacttgggcaggagtggaagccataataagaattctgcaacaactgctgtttattcatttcagaattgggtgtcaacatagcagaatagacattcttcgacgaaggagagcaagaaatggagccagtagatcctagactagagccctggaagcatccaggaagtcagcctaggactgcttgtaccaattgctattgtaaaaagtgttgctttcattgccaagtttgtttcataacaaaaggcttaggcatctcctatggcaggaagaagcggagacagcgacgaagagctcctcaagacagtcagactcatcaagtttctctatcaaagcagtaagtagtacatgtaatgcaatctttacaaatattagcagtagtagcattagtagtagcagcaataatagcaatagttgtgtggtccatagtattcatagaatataggaaaataagaagacaaaacaaaatagaaaggttgattgatagaataatagaaagagcagaagacagtggcaatgagagtgacggagatcaggaagaattatcagcacttgtggaaatggggcacgatgctccttgggatgttaatgatctgtaaagctgcagaaaatttgtgggtcacagtttattatggggtacctgtgtggaaagaagcaaccaccactctattttgtgcctcagatgctaaagcgtatgatacagaggtacataatgtttgggccacacatgcctgtgtacccacagaccccaacccacaagaagtagaactgaagaatgtgacagaaaattttaacatgtggaaaaataacatggtagaccaaatgcatgaggatataattagtttatgggatcaaagcctaaagccatgtgtaaaattaaccccactctgtgttactttaaattgcactgattatgggaatgatactaacaccaataatagtagtgctactaaccccactagtagtagcgggggaatggaggggagaggagaaataaaaaattgctctttcaatatcaccagaagcataagagataaagtgaagaaagaatatgcacttttttatagtcttgatgtaataccaataaaagatgataatactagctataggttgagaagttgtaacacctcagtcattacacaggcctgtccaaaggtatcctttgaaccaattcccatacattattgtgccccggctggttttgcgattctaaagtgtaatgataaaaagttcaatggaaaaggaccatgtacaaatgtcagcacagtacaatgtacacatggaattaggccagtagtatcaactcaactgctgttaaatggcagtctagcagaagaagaggtagtaattagatcagacaatttctcggacaatgctaaagtcataatagtacatctgaatgaatctgtagaaattaattgtacaagactcaacaacattacaaggagaagtatacatgtaggacatgtaggaccaggcagagcaatttatacaacaggaataataggaaaaataagacaagcacattgtaacattagtagagcaaaatggaataacactttaaaacagatagttacaaaattaagagaacaatttaagaataaaacaatagtctttaatcaatcctcaggaggggacccagaaattgtaatgcacagttttaattgtggaggggaatttttctactgtaattcaacacaactgtttaacagtacttggaatggtactgcatggtcaaataacactgaaggaaatgaaaatgacacaatcacactcccatgcagaataaaacaaattataaacatgtggcaggaagtaggaaaagcaatgtatgcacctcccatcagaggacaaattagatgttcatcaaatattacagggctgatattaacaagagatggtggtattaaccagaccaacaccaccgagattttcaggcctggaggaggagatatgaaggacaattggagaagtgaattatataaatataaagtagtaaaaattgaaccattaggagtagcacccaccaaggcaaagagaagagtggtgcaaagagaaaaaagagcagtgggaataataggagctatgctccttgggttcttgggagcagcaggaagcactatgggcgcagcgtcaatgacgctgacggtacaggccagacaattattgtctggtatagtgcaacagcagaacaatttgctgagggctattgaggcgcaacagcatctgttgcacctcacagtctggggcatcaagcagctccaagcaagagtcctggctgtggaaagatacctaagggatcaacagctcctggggttttggggttgctctggaaaactcatttgcaccactgctgtgccttggaatactagttggagtaataaatctctgagtcagatttgggataacatgacctggatgcagtgggaaagggaaattgataattacacaagcttaatatacaacttaattgaagaatcgcaaaaccaacaagaaaagaatgaacaagagttattggaattagataactgggcaagtttgtggaattggtttagcataacaaattggctgtggtatataaaaatattcataatgatagtaggaggcttggtaggtttaagaatagtttttactgtactttctatagtaaatagagttaggcagggatactcaccattgtcgtttcagacgcgcctcccagccaggaggggacccgacaggcccgaaggaatcgaagaagaaggtggagagagagacagagacagatccggtcaattagtggatggattcttagcaattatctgggtcgacctgcggagcctgtgcctcttcagctaccaccgcttgagagacttactcttgattgtaacgaggattgtggaacttctgggacgcagggggtgggaagccctcaaatattggtggaatctcctacaatattggattcaggaactaaagaatagtgctgttagcttgctcaacgccacagccatagcagtagctgagggaactgatagggtgggtctctcttgttagaccagatctgagcctgggagctctctggctaactagggaacccactgcttaagcctcaataaagcttgccttgagtgcttcaagtagtgtgtgcccgtctgttgtgtgactctgatagctagagatcccttcagaccaaatttagtcagtgtgaaaaatctctagcagtggcgcctgaacagggacttgaaagcgaaagagaaaccagagaagctctctcgacgcaggactcggcttgctgaagcgcgcacggcaagaggcgaggggacggcgactggtgagtacgccaaaattttgactagcggaggctagaaggagagagatgggtgcgagagcgtcgatattaagcgggggaggattagatagatgggaaaaaattcggttaaggccagggggaaagaaaaaatatagattaaaacatttagtatgggcaagcagggagctagaacgattcgcagtcaatcctggcctattagaaacatcagaaggttgtagacaaatactgggacaactacaaccagcccttcagacaggatcagaagaacttagatcattatataatacagtagcaaccctctattgtgtgcatcaaaagatagatgtaaaagacaccaaggaagctttagataagatagaggaagagcaaaacaaaagtaagaaaaaagcacagcaagcagcagctgacacaggaaatagcagccaggtcagccaaaattaccccatagtgcagaacatccaggggcaaatggtacatcaggccatatcacctagaactttaaatgcatgggtaaaagtagtagaagagaaggctttcagcccagaagtaatacccatgttttcagcattatcagaaggagccaccccacaagatttaaacaccatgctaaacacagtggggggacatcaagcagccatgcaaatgttaaaagagaccatcaatgaggaagctgcagaatgggatagattgcatccagtgcatgcagggcctcatccaccaggccagatgagagaaccaaggggaagtgacatagcaggaactactagtacccttcaggaacaaatagcatggatgacaaataatccacctatcccagtaggagaaatctataagagatggataatcctgggattaaataaaatagtaaggatgtatagccctaccagcattctggacataaaacaaggaccaaaggaaccctttagagactatgtagaccggttctataagactctaagagccgagcaagcttcacaggaggtaaaaaattggatgacagaaaccttgttggtccaaaatgcgaacccagattgtaagactattttaaaagcattgggaccagcagctacactagaagaaatgatgacagcatgtcagggagtgggaggacccggccataaagcaagagttttggcagaagcaatgagccaagtaacaaattcagctaccataatgatgcagaaaggcaattttaggaaccaaagaaaaattgttaagtgtttcaattgtggcaaagaagggcacatagccaaaaattgcagggcccctaggaaaaggggctgttggaaatgtggaaaggagggacaccaaatgaaagattgtactgagagacaggctaattttttagggaaaatctggccttcccacaggggaaggccagggaattttcctcagaacagactagagccaacagccccaccagccccaccagaagagagcttcaggtttggggaagagacaacaactccctctcagaagcaggagctgatagacaaggaactgtatccttcagcttccctcaaatcactctttggcaacgaccccttgtcacaataaagataggggggcaactaaaggaagctctattagatacaggagcagatgatacagtattagaagaaataaatttgccaggaagatggaaaccaaaaatgatagggggaattggaggttttatcaaagtaagacagtatgatcaaatactcgtagaaatctgtggacataaagctataggtacagtattagtaggacctacacctgtcaacataattggaagaaatctgttgactcagattggttgcactttaaattttcccattagtcctattgaaactgtaccagtaaaattaaagccaggaatggatggcccaaaagttaaacaatggccattgacagaagaaaaaataaaagcattagtagaaatctgtacagaaatggaaaaggaaggaaaaatttcaaaaatcgggcctgaaaatccatataatactccagtatttgccataaagaaaaaagacagtactaaatggagaaaattagtagatttcagagaacttaataagaaaactcaagacttctgggaagttcaattaggaataccacatcccgcagggttaaaaaagaaaaaatcagtaacagtactggatgtgggtgatgcatatttttcagttcccttagataaagaattcaggaagtacactgcatttaccatacctagtataaacaatgagacaccagggattagatatcagtacaatgtgcttccacagggatggaaaggatcaccagcaatattccaaagcagcatgacaaaaatcttagagccttttagaaaacaaaatccagacatagttatctatcaatacatggacgatttgtatgtaggatctgacttagaaatagggcagcatagaacaaaaatagaggaactgagacaacatctgttgaagtggggatttaccacaccagacaaaaaacatcagaaagaacctccattcctttggatgggttatgaactccatcctgataaatggacagtacagcctatagtgctgccagaaaaggacagctggactgtcaatgacatacagaagttagtgggaaaattgaattgggcaagtcagatttacccagggattaaagtaaagcaattatgtagactccttaggggaaccaaggcactaacagaagtaataccactaacaaaagaagcagagctagaactggcagaaaacagggaaattctaaaagaaccagtacatggagtgtattatgacccatcaaaagacttaatagcggaaatacagaagcaggggcaaggtcaatggacatatcaaatttatcaagagccatttaaaaatctgaaaacaggaaaatatgcaagaatgaggggtgcccacactaatgatgtaaaacaattaacagaggcagtgcaaaaaataaccacagaaagcatagtaatatggggaaagactcctaaatttaaactacccatacaaaaagaaacatgggaaacatggtggacagagtattggcaagccacctggattcctgagtgggagtttgtcaatacccctcccttagtaaaattatggtaccagttagagaaagaacccataataggagcagaaactttctatgtagatggggcagctaacagggagactaaattaggaaaagcaggatatgttactaacaaagggagacaaaaagttgtctccataactgacacaacaaatcagaagactgagttacaagcaattcttctagcattacaggattctggattagaagtaaacatagtaacagactcacaatatgcattaggaatcattcaagcacaaccagataaaagtgaatcagagatagtcagtcaaataatagagcagttaataaaaaaagaaaaggtctacctgacatgggtaccagcgcacaaaggaattggaggaaatgaacaagtagataaattagtcagtactggaatcaggaaagtactctttttagatggaatagataaagcccaagaagaacatgaaaaatatcacagtaattggagggcaatggctagtgattttaacctgccacctgtggtagcaaaagagatagtagccagctgtgataaatgtcagctaaaaggagaagccatgcatggacaagtagactgtagtccaggaatatggcaactagattgtacacatttagaaggaaaaattatcctggtagcagttcatgtagccagtggatatatagaagcagaagttattccagcagaaacagggcaggaaacagcatactttctcttaaaattagcaggaagatggccagtaaaaacagtacatacagacaatggcagcaatttcaccagtactacagttaaggccgcctgttggtgggcaggaatcaagcaggaatttggcattccctacaatccccaaagtcaaggagtagtagaatctataaataaagaattaaagaaagttataggacagataagagatcaggctgaacatcttaagacagcagtacaaatggcagtattcatccacaattttaaaagaaaaggggggattggggggtacagtgcaggggaaagaatagtagacataatagcaacagacatacaaactaaagaactacaaaaacaaattacaaaaattcaaaattttcgggtttattacagggacagcagagatccactttggaaaggaccagcaaagcttctctggaaaggtgaaggggcagtagtaatacaagataatagtgacataaaagtagtgccaagaagaaaagcaaagatcattagggattatggaaaacagatggcaggtgatgattgtgtggcaagtagacaggatgaggattagaacatggaaaagtttagtaaaacaccatatgtatgtttcaaggaaagctaagggatggttttatagacatcactatgaaagtactcatccgagaataagttcagaagtacacatcccactagggaatgcaaaattggtaataacaacatattggggtctacatacaggagaaagagactggcatttgggtcaaggagtctccatagaattgaggaaaaggagatatagcacacaattagaccctaacctagcagaccaactaattcatctgcattactttgattgtttttcagaatctgctataagaaatgccatattaggacatatagttagccctaggtgtgaatatcaagcaggacataacaaggtaggatctctacagtacttggcactaacagcattagtaagaccaagaaaaaagataaagccacctttgcctagtgttacaaaactgacagaggatagatggaacaagccccagaagaccaagggccacaaagggaaccatacaatgaatggacactagaacttttagaggagctcaagaatgaagctgttagacattttcctaggatatggctccatagcttagggcaacatatctatgaaacttatggagatacttgggcaggagtggaagccataataagaattctgcaacaactgctgtttattcatttcagaattgggtgtcaacatagcagaatagacattcttcgacgaaggagagcaagaaatggagccagtagatcctagactagagccctggaagcatccaggaagtcagcctaggactgcttgtaccaattgctattgtaaaaagtgttgctttcattgccaagtttgtttcataacaaaaggcttaggcatctcctatggcaggaagaagcggagacagcgacgaagagctcctcaagacagtcagactcatcaagtttctctatcaaagcagtaagtagtacatgtaatgcaatctttacaaatattagcagtagtagcattagtagtagcagcaataatagcaatagttgtgtggtccatagtattcatagaatataggaaaataagaagacaaaacaaaatagaaaggttgattgatagaataatagaaagagcagaagacagtggcaatgagagtgacggagatcaggaagaattatcagcacttgtggaaatggggcacgatgctccttgggatgttaatgatctgtaaagctgcagaaaatttgtgggtcacagtttattatggggtacctgtgtggaaagaagcaaccaccactctattttgtgcctcagatgctaaagcgtatgatacagaggtacataatgtttgggccacacatgcctgtgtacccacagaccccaacccacaagaagtagaactgaagaatgtgacagaaaattttaacatgtggaaaaataacatggtagaccaaatgcatgaggatataattagtttatgggatcaaagcctaaagccatgtgtaaaattaaccccactctgtgttactttaaattgcactgattatgggaatgatactaacaccaataatagtagtgctactaaccccactagtagtagcgggggaatggaggggagaggagaaataaaaaattgctctttcaatatcaccagaagcataagagataaagtgaagaaagaatatgcacttttttatagtcttgatgtaataccaataaaagatgataatactagctataggttgagaagttgtaacacctcagtcattacacaggcctgtccaaaggtatcctttgaaccaattcccatacattattgtgccccggctggttttgcgattctaaagtgtaatgataaaaagttcaatggaaaaggaccatgtacaaatgtcagcacagtacaatgtacacatggaattaggccagtagtatcaactcaactgctgttaaatggcagtctagcagaagaagaggtagtaattagatcagacaatttctcggacaatgctaaagtcataatagtacatctgaatgaatctgtagaaattaattgtacaagactcaacaacattacaaggagaagtatacatgtaggacatgtaggaccaggcagagcaatttatacaacaggaataataggaaaaataagacaagcacattgtaacattagtagagcaaaatggaataacactttaaaacagatagttacaaaattaagagaacaatttaagaataaaacaatagtctttaatcaatcctcaggaggggacccagaaattgtaatgcacagttttaattgtggaggggaatttttctactgtaattcaacacaactgtttaacagtacttggaatggtactgcatggtcaaataacactgaaggaaatgaaaatgacacaatcacactcccatgcagaataaaacaaattataaacatgtggcaggaagtaggaaaagcaatgtatgcacctcccatcagaggacaaattagatgttcatcaaatattacagggctgatattaacaagagatggtggtattaaccagaccaacaccaccgagattttcaggcctggaggaggagatatgaaggacaattggagaagtgaattatataaatataaagtagtaaaaattgaaccattaggagtagcacccaccaaggcaaagagaagagtggtgcaaagagaaaaaagagcagtgggaataataggagctatgctccttgggttcttgggagcagcaggaagcactatgggcgcagcgtcaatgacgctgacggtacaggccagacaattattgtctggtatagtgcaacagcagaacaatttgctgagggctattgaggcgcaacagcatctgttgcacctcacagtctggggcatcaagcagctccaagcaagagtcctggctgtggaaagatacctaagggatcaacagctcctggggttttggggttgctctggaaaactcatttgcaccactgctgtgccttggaatactagttggagtaataaatctctgagtcagatttgggataacatgacctggatgcagtgggaaagggaaattgataattacacaagcttaatatacaacttaattgaagaatcgcaaaaccaacaagaaaagaatgaacaagagttattggaattagataactgggcaagtttgtggaattggtttagcataacaaattggctgtggtatataaaaatattcataatgatagtaggaggcttggtaggtttaagaatagtttttactgtactttctatagtaaatagagttaggcagggatactcaccattgtcgtttcagacgcgcctcccagccaggaggggacccgacaggcccgaaggaatcgaagaagaaggtggagagagagacagagacagatccggtcaattagtggatggattcttagcaattatctgggtcgacctgcggagcctgtgcctcttcagctaccaccgcttgagagacttactcttgattgtaacgaggattgtggaacttctgggacgcagggggtgggaagccctcaaatattggtggaatctcctacaatattggattcaggaactaaagaatagtgctgttagcttgctcaacgccacagccatagcagtagctgagggaactgatagggt

  4. Public Database Content (Sources: PDB, EBI, SIB)

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

  6. The KB Protein Model Portal • 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.

  7. The KB Protein Model Portal • 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;

  8. The KB Protein Model Portal 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

  9. The KB Protein Model Portal 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.

  10. The KB Protein Model Portal 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.

  11. The KB Protein Model Portal CRC64: D3B6F5D13FF7422D MD5: b6f2c321d42d50b985186307434b5166 UPI: UPI0000000CB5 Real time annotation Database Entry Version Organism First Seen Last Seen Active UniProtKB/Swiss-Prot P68399 1 Bos taurus (Bovine) 2004-11-23 2007-07-24 Yes UniProtKB/Swiss-Prot P68400 1 Homo sapiens (Human) 2004-11-23 2007-07-24 Yes UniProtKB/Swiss-Prot P19138 1 1990-11-01 2004-11-09 No UniProtKB/TrEMBL Q5U065 1 Homo sapiens (Human) 2005-05-10 2007-07-24 Yes TrEMBLnew AAH53532 2003-06-14 2003-08-30 No TrEMBLnew AAH11668 2003-03-29 2003-06-14 No International Protein Index (IPI) IPI00016613 1 2003-03-14 2004-11-15 No International Protein Index (IPI) IPI00744507 1 Homo sapiens (Human) 2006-05-16 2007-06-29 Yes International Protein Index (IPI) IPI00707334 1 Bos taurus (Bovine) 2006-01-24 2007-06-29 Yes RefSeq NP_808227 1 2004-07-08 2007-05-08 Yes RefSeq NP_001886 1 2004-09-24 2007-05-08 No RefSeq NP_777060 1 2004-09-14 2006-02-19 No RefSeq XP_850579 1 2005-08-31 2007-05-08 Yes RefSeq XP_001112324 1 2006-06-15 2007-05-08 Yes RefSeq XP_001112363 1 2006-06-15 2007-05-08 Yes Ensembl ENSCAFP00000010339 Canis familiaris (Dog) 2004-12-09 2007-06-04 Yes Ensembl ENSP00000217244 Homo sapiens (Human) 2003-04-01 2007-05-31 Yes Ensembl ENSP00000339247 Homo sapiens (Human) 2004-05-12 2007-05-31 Yes Ensembl ENSP00000341595 2006-04-03 2006-09-27 No Ensembl ENSMMUP00000037659 Macaca mulatta (Rhesus macaque) 2006-08-01 2007-06-04 Yes EMBL Annotated CONs EAX10665 1 Homo sapiens (Human) 2007-01-15 2007-06-12 Yes EMBL CDS AAA35503 1 Homo sapiens (Human) 2003-03-12 2007-06-20 Yes PIR-PSD Archive A30319 2003-03-31 2003-04-04 Yes European Patent Office (EPO) CS458506 1 2007-03-20 2007-06-09 Yes US Patent Office (USPO) AAE81305 1 2003-03-26 2007-06-01 Yes Japan Patent Office (JPO) BD879267 2007-01-11 2007-06-01 Yes TROME NT_011387_19_8 2004-08-23 2004-08-28 No H-Invitational Database (H-InvDB) HIT000053902 3 Homo sapiens (Human) 2006-07-02 2006-07-02 No CRC64: A3B6F5D13DF7422E MD5: 605f4802e88ec1443d36520ac05df3b9 UPI: UPI0000044948 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|IPI00707334|IPI00707334.1 CASEIN KINASE II SUBUNIT ALPHA. MSGPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINIT NNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTD FKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAE FYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYD QLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDF LDKLLRYDHQSRLTAREAMEHPYFYTVVKDQARMGSSSMPGGSTPVSSANMMSGISSVPT PSPLGPLAGSPVIAAANPLGMPVPAAAGAQQ

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

  13. http://www.proteinmodelportal.org

  14. The KB Protein Model Portal

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

  16. 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

  17. Outlook: Next steps • New Features & Functions • Better visualization of query results

  18. 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

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

  20. 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

  21. 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. • modeling_workshop@psi-structuralgenomics.org

  22. 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 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 Funding: NIH – National Institutes of Health SIB – Swiss Institue of Bioinformatics

More Related