1. Bioinformatics Tools - Dr Jaime Prilusky - 2006 Bioinformatics Tools for Structural Biolog Bioinformatics Tools for Structural Biology Dr Jaime Prilusky ISPC-WIS Helsinki, June 2006

2. Bioinformatics Tools - Dr Jaime Prilusky - 2006 http://www.weizmann.ac.il/ISPC/biotools.html Target Identity and Foldability Selection of Expression System Selection of Crystallization Conditions Data Awarness Data Management

3. Bioinformatics Tools - Dr Jaime Prilusky - 2006 http://www.weizmann.ac.il/ISPC/biotools.html Web’s Services

4. Bioinformatics Tools - Dr Jaime Prilusky - 2006 BestPrimers (just best primers) FoldIndex (will this protein fold?) HyPare (detects hot-spots for mutation) LabTargets (browser/database for proteomics) OCA (browser/database for structure & function) RecentReferences (what people published?) SeqAlert (someone else works on this sequence?) SeqFacts (tell me something about this sequence) SuggestES (suggest an expression system) SuggestXC (suggest crystallization conditions) VerifyCloning (check results from DNA sequencing) Some of our tools:

5. Bioinformatics Tools - Dr Jaime Prilusky - 2006 FoldIndex FoldIndex© tries to answer to the question: Will this protein fold? FoldIndex© predicts whether a given protein is intrinsically disordered. Prilusky J., Felder C.E., Zeev-Ben-Mordehai T., Rydberg E., Man O., Beckmann J.S., Silman I. and Sussman J.L. Bioinformatics, 2005 Aug 15;21(16):3435-8 http://bip.weizmann.ac.il/fold Web Services Enabled

6. Bioinformatics Tools - Dr Jaime Prilusky - 2006 natively unfolded folded Why are natively unfolded proteins unstructured under physiologic conditions? Vladimir N. Uversky, Joel R. Gillespie, Anthony L. Fink; Proteins: Structure, Function, and Genetics, Volume 41, Issue 3, Pages 415-427

7. Bioinformatics Tools - Dr Jaime Prilusky - 2006

9. Web Services’ access to FoldIndex: http://bip.weizmann.ac.il/fldbin/findex?sq=SEQ&m=xml sq is the protein sequence, one character, no spaces. m (mode) is either xml or efam, the format FoldIndex will return the result on. With the mode set to ‘xml’, the server sends results in XML format. When mode is equal to ‘efam’, the results are sent in eFamily format. FoldIndex home page has sample Perl scripts to retrieve and parse prediction data. Web Services Enabled

10. Bioinformatics Tools - Dr Jaime Prilusky - 2006 SeqFacts© SeqFacts© is a tool for sequence identification, analysis, characterization and annotation. This server will try to find relevant information related to your sequence. http://bip.weizmann.ac.il/sqfbin/seqfacts

11. Bioinformatics Tools - Dr Jaime Prilusky - 2006

14. sequence properties references DB similarity RecentReferences SeqAlert(once) FoldIndex SeqFacts RecentReferences Amino AcidDNA similarity search specific DB search quality cleaning vectors removal calculation ORF

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16. Automatic analysis of 1226_int11f-SP6-19 (Sun Jun 8 15:55:24 2003) ------------------------------------------------------------------------------- Summary: This analysis is based on a clean portion (4 to 644) from the 920 original bases. The best ORF of the six frames translation has a length of 186. A similarity search found 50 hits on 18 organisms: Oryctolagus cuniculus and Homo sapiens are the most representatives. Conserved domains present in the translated sequence: Arylesterase, COG3386. Original files: 1226_int11f-SP6-19.fasta 1226_int11f-SP6-19.gcg ORFs Six Frames translation Similarity Search Conserved Domain database Genome Drosophila Genome Homo Genome Mus Genome Rattus Fantom (Functional Annotation Of Mouse) Taxonomy

17. Bioinformatics Tools - Dr Jaime Prilusky - 2006 Automatic analysis of 1226_int11f-SP6-19 (Sun Jun 8 15:55:24 2003) ------------------------------------------------------------------------------- Summary: This analysis is based on a clean portion (4 to 644) from the 920 original bases. The best ORF of the six frames translation has a length of 186. A similarity search found 50 hits on 18 organisms: Oryctolagus cuniculus and Homo sapiens are the most representatives. Conserved domains present in the translated sequence: Arylesterase, COG3386. Original files: 1226_int11f-SP6-19.fasta 1226_int11f-SP6-19.gcg ORFs Six Frames translation Similarity Search Conserved Domain database Genome Drosophila Genome Homo Genome Mus Genome Rattus Fantom (Functional Annotation Of Mouse) Taxonomy

18. Bioinformatics Tools - Dr Jaime Prilusky - 2006 Automatic analysis of 1226_int11f-SP6-19 (Sun Jun 8 15:55:24 2003) ------------------------------------------------------------------------------- Summary: This analysis is based on a clean portion (4 to 644) from the 920 original bases. The best ORF of the six frames translation has a length of 186. A similarity search found 50 hits on 18 organisms: Oryctolagus cuniculus and Homo sapiens are the most representatives. Conserved domains present in the translated sequence: Arylesterase, COG3386. Original files: 1226_int11f-SP6-19.fasta 1226_int11f-SP6-19.gcg ORFs Six Frames translation Similarity Search Conserved Domain database Genome Drosophila Genome Homo Genome Mus Genome Rattus Fantom (Functional Annotation Of Mouse) Taxonomy

19. Bioinformatics Tools - Dr Jaime Prilusky - 2006 Automatic analysis of 1226_int11f-SP6-19 (Sun Jun 8 15:55:24 2003) ------------------------------------------------------------------------------- Summary: This analysis is based on a clean portion (4 to 644) from the 920 original bases. The best ORF of the six frames translation has a length of 186. A similarity search found 50 hits on 18 organisms: Oryctolagus cuniculus and Homo sapiens are the most representatives. Conserved domains present in the translated sequence: Arylesterase, COG3386. Original files: 1226_int11f-SP6-19.fasta 1226_int11f-SP6-19.gcg ORFs Six Frames translation Similarity Search Conserved Domain database Genome Drosophila Genome Homo Genome Mus Genome Rattus Fantom (Functional Annotation Of Mouse) Taxonomy

20. Bioinformatics Tools - Dr Jaime Prilusky - 2006 BestPrimers BestPrimers© provides a simple interface for primers calculation, with FoldIndex© support. http://bip.weizmann.ac.il/sqfbin/bestPrimers Web Services Enabled

21. Bioinformatics Tools - Dr Jaime Prilusky - 2006

23. VerifyCloning © VerifyCloning© compares your original sequence against the result from cloning procedures, highlighting conflicting areas. VerifyCloning has an automatic reverse/complement mode that will reorder your sequences if required. http://bip.weizmann.ac.il/vfclon Web Services Enabled

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26. SuggestES © SuggestES© takes the protein sequence you provide and scans a large database with protein sequences with known results for different expression systems, generating a suggestion based on several parameters: Similarity: how similar is your sequence to the existing data in the database? Recentness: how recently was a given expression system used? Frequency: how frequently was a given expression system used? http://bip.weizmann.ac.il/suggestES Web Services Enabled

27. Bioinformatics Tools - Dr Jaime Prilusky - 2006

28. SuggestXC © SuggestXC© takes the protein sequence you provide and scans a large database with protein sequences with known results for different crystallization conditions, generating a suggestion based on several parameters: Similarity: how similar is your sequence to the existing data in the database? Recentness: how recently was a given crystallization condition used? Frequency: how frequently was a given crystallization condition used? http://bip.weizmann.ac.il/suggestXC Web Services Enabled

29. Bioinformatics Tools - Dr Jaime Prilusky - 2006 HyPare© Hypare© is a newly designed tool based on the PARE algorithm (Predicting Association Rate Enhancement). With HyPare you can find hotspots for association, and thus, engineer your proteins for faster and tighter binding http://bip.weizmann.ac.il/hypare Web Services Enabled

30. Bioinformatics Tools - Dr Jaime Prilusky - 2006 SeqAlert SeqAlert© is a sequence alerting service that will periodically compare your sequence(s) against sequences from determined 3D structures, or structures being determined at PDB, and TargetDB, the database of target sequences from worldwide structural genomics projects. It also reports the Pubmed IDs of papers that might be related to your sequence, published on the last 20 days. http://bip.weizmann.ac.il/seqalert

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33. Proteomics LIMS An integrated Laboratory Information Management Systems for Proteomics with Complexes support. Web Services Enabled http://www.weizmann.ac.il/ISPC/

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41. LabTargets (browser/database for proteomics) supported operating systems required software client-server architecture generates/exports SPINE xml TargetDB xml Targets Status Graph Targets Detail Structures Gallery

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47. Direct Web Access Web Services, Bulk Access Web Services, Software Integration How can you access our tools?

48. Bioinformatics Tools - Dr Jaime Prilusky - 2006 OCA mirrors world distribution Direct Web Access http://bip.weizmann.ac.il/oca

49. Bioinformatics Tools - Dr Jaime Prilusky - 2006 Web Services, Bulk Access Beer Sheva, Israel Cambridge, USA Chicago, USA Hawaii, USA Helsinki, Finland Leipzig, Germany Missouri, USA Montpellier, France San Diego, USA Bangalore, India Kansas City, USA Madrid, Spain FoldIndex LPC CSU OCA

50. Bioinformatics Tools - Dr Jaime Prilusky - 2006 Web Services, Software Integration IBS: Integrated Bioinformatics System @ KISTI, Daejeon, South Korea [FoldIndex, BestPrimers, SeqFacts, SuggestES] GUTSS: Genome Structure Selection System @ The Burham Institute, La Jolla CA, USA [SeqFacts] Raptor 3D: functional annotations to structures @ GBF, Braunschweig, Germany [OCA] WIS LIMS: @ Weizmann Institute, Rehovot, Israel [OCA, FoldIndex, SeqFacts, BestPrimers, …]

51. Bioinformatics Tools - Dr Jaime Prilusky - 2006 Some of our tools allow for a local installation Why to have a local installation? intranet requirements repetitive batch analysis tight services integration

52. Bioinformatics Tools - Dr Jaime Prilusky - 2006 OCA OCA© facilitates the understanding of the genomics/proteomics biological data through data analysis and synthesis. The data integration process brings together dispersed pieces of information, generating comprehensive summaries that might be just what a researcher needs for crystallizing an idea or understanding a problem. http://bip.weizmann.ac.il/oca Web Services Enabled

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56. Dr. Shira Albeck Rani Bravdo Prof. Yigal Burstein Dr. Orly Dym Yossi Jacobovitch Dorit Kalo Nurit Levy Ran Meged Yigal Michael Dr. Yoav Peleg Dr. Jaime Prilusky Prof. Gideon Schreiber Prof. Israel Silman Prof. Joel L Sussman Dr. Tamar Unger Israel Structural Proteomics Center

57. Bioinformatics Tools - Dr Jaime Prilusky - 2006 Dr Jaime Prilusky Jaime.Prilusky@weizmann.ac.il

58. Bioinformatics Tools - Dr Jaime Prilusky - 2006