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PSIMAP : protein structural interactome map


About PSIMAP

PSIMAP is a tool and DB for constructing interactomes. It is a general protocol of mapping proteins and their family interactions. The first map created was called 'pdb-sin' as it was based on PDB database (PDB structural interaction network). It was the first protocol that could map the global molecular interactions using protein domain (family) structural folds.

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Contents

PSIMAP and its sub projects

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Publication of PSIMAP related papers

  1. Jefferson, E. R., Walsh, T. P. and Barton, G. J. (2006)
    "Biological units and their effect upon the properties and prediction of protein-protein interactions", J. Mol. Biol., 364, 1118-1129.
  2. PSIbase: a database of Protein Structural Interactome map (PSIMAP). (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15749693) Gong S, Yoon G, Jang I, Bolser D, Dafas P, Schroeder M, Choi H, Cho Y, Han K, Lee S, Choi H, Lappe M, Holm L, Kim S, Oh D, Bhak J. Bioinformatics. 2005 Mar 3
  3. Architecture of basic building blocks in protein and domain structural interaction networks (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15613386). Moon HS, Bhak J, Lee KH, Lee D.Bioinformatics. 2005 Apr 15;21(8):1479-86. Epub 2004 Dec 21.
  4. Using convex hulls to extract interaction interfaces from known structures. (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15231539) Panos Dafas, Dan Bolser, Jacek Gomoluch, Jong Park and Michael Schroeder, Bioinformatics. 10 July 2004. 20(10):1486-1490.
  5. HPID: The Human Protein Interaction Database. (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15117749) Kyungsook Han, Byungkyu Park, Hyongguen Kim, Jinsun Hong and Jong Park, Bioinformatics, 29 Apr. 2004 (In press)
  6. Large scale co-evolution analysis of Protein Structural Interlogues using the global Protein Structural Interactome Map(PSIMAP). (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14764552) Wankyu Kim, Dan M. Bolser and Jong Park, Bioinformatics, 2004, 20(7):1138-1150.
  7. Visualisation and Graph-theoretic Analysis of a Large-scale Protein Structural Interactome. (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14531933) Dan M Bolser, Panos Dafas, Richard Harrington, Jong Park and Michael Schroeder, BMC Bioinformatics, 8 October 2003, 4;45:1471-2105.
  8. Visualization and Analysis of Protein Interactions. (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12538268) Byonghyon Ju, ByungkyuPark, Jong Park and Kyungsook Han, Bioinformatics, 2003, 19:317-318.
  9. Predicting Protein Interactions in Human by Homologous Interactions in Yeast. Hyongguen Kim, Jong Park and Kyungsook Han, Lecture Notes in Computer Science, 2003, 2637:159-165.
  10. Network Biology (http://networkbiology.net): Datamining Biological Networks. IEEE Intelligent Systems (http://csdl.computer.org/comp/mags/ex/2002/03/x3toc.htm), May/June (Vol. 17, No. 3, pp66-80). 2002
  11. The Conservation of Protein Interaction Network in Evolution. (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11791232&dopt=Abstract) GIW2001 (http://www.jsbi.org/journal/GIW01/GIW01F14.html): The Twelfth International Conference on Genome Informatics, Tokyo Japan, 2001.
  12. Generating protein interactioin map from incomplete data: application of fold assignment. (http://bio.cc/PSIMAP/Paper/PSIMAP_bioinformatics_2001.html) Lappe M, Park J, Niggemann O, Holm L. Bioinformatics. 2001;17 Suppl 1:S149-56. PMID: 11473004 (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11473004&dopt=Abstract) [PubMed - indexed for MEDLINE]. PDF file (http://bio.cc/PSIMAP/Paper/bioinformatics_paper_for_fold_assignment_2001.pdf)
  13. Mapping Protein Family Interactions: Intramolecular and Intermolecular Protein Family Interaction Repertoires in the PDB and Yeast , Jong Park, Michael Lappe & Sarah A. Teichmann, Journal of Molecular Biology (2001). PDF file (http://bio.cc/Publish/Paper/JMB_published_PSIMAP.pdf)
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PSIMAP People

  • People who have been involved in PSIMAP in various ways. It is an open & free collaboration of people.
    • Any of you! Please email us if you want to contribute and want to participate in this research and writing papers with us.
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Major Directory

MIPS_vs_SISF -> the working dir. Paper -> for paper /DB/PDB/PDB100


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Important files

  • (1) Making the first interaction list. make_scop_domain_interaction_pair_table.pl result_pair_skip.psdip (THE output)
    • Whole chain - chain (upon Sarah's request)
    • Whole chain - Motif (fragment)
    • Motif - Motif
  • dir.dom.scop.txt_1.48


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Data files

  1. result_pair_skip.psdip.gz /DB/PDB/PDB100
  2. result_pair_skip_chain_domain.psdip.gz
  3. result_pair_skip_chain_motif_domain.psdip.gz
  4. result_pair_skip_combined_motif_domain.psdip.gz
  5. result_pair_skip_motif_domain.psdip.gz
  6. consistent_expression_cluster.txt (http://bio.cc/PSIMAP/consistent_expression_cluster.txt) (from Sonia)
  7. versatility_summary_100_sorted_comma.piver
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Services

  1. PSIbase server (http://psibase.kobic.re.kr)


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File Extensions

  1. PSDIP : protein structural domain interaction pair
  2. PIVER : Protein Interaction Versatility


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BiO Interact Refer , FAQs, Papers

  1. Paper (http://bio.cc/PSIMAP/Paper/): (/Paper/PSIFA_paper.html)
    1. Paper/comp_bio_str_inter_map.html
    2. Paper/SCOP domain interaction table
    3. Word Doc file (edited in VMWARE)
  2. References for interaction studies


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Related Research


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Misc

Contact: Jong Bhak, j@bio.cc, jong@kribb.re.kr, Sungsam Gong, ssgong@bio.cc


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