fatcat.godziklab.org

FATCAT - Godzik's lab

Ligned fragment pairs allowing T. Protein structures are flexible and undergo structural rearrangements as part of their function. FATCAT ( F. Ligned fragment pairs allowing T. Yuzhen Ye and Adam Godzik. Flexible structure alignment by chaining aligned fragment pairs allowing twists. 2003. Bioinformatics vol.19 suppl. 2. ii246-ii255. ( more. FATCAT Database Searching;. Flexible Structural Neighborhood (FSN). For multiple flexible structure comparison.

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FATCAT - Godzik's lab | fatcat.godziklab.org Reviews

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Ligned fragment pairs allowing T. Protein structures are flexible and undergo structural rearrangements as part of their function. FATCAT ( F. Ligned fragment pairs allowing T. Yuzhen Ye and Adam Godzik. Flexible structure alignment by chaining aligned fragment pairs allowing twists. 2003. Bioinformatics vol.19 suppl. 2. ii246-ii255. ( more. FATCAT Database Searching;. Flexible Structural Neighborhood (FSN). For multiple flexible structure comparison.

<META> KEYWORDS

1 lexible structure a

2 lignmen t

3 by c

4 haining a

5 wists

6 fatcat home

7 pairwise alignment

8 database searching

9 structural neighbors

10 references

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lexible structure a,lignmen t,by c,haining a,wists,fatcat home,pairwise alignment,database searching,structural neighbors,references,introduction,documents,algorithm paper,fatcat report;,fatcat benchmarking,reference,services,fatcat pairwise alignment

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FATCAT - Godzik's lab | fatcat.godziklab.org Reviews

https://fatcat.godziklab.org

Ligned fragment pairs allowing T. Protein structures are flexible and undergo structural rearrangements as part of their function. FATCAT ( F. Ligned fragment pairs allowing T. Yuzhen Ye and Adam Godzik. Flexible structure alignment by chaining aligned fragment pairs allowing twists. 2003. Bioinformatics vol.19 suppl. 2. ii246-ii255. ( more. FATCAT Database Searching;. Flexible Structural Neighborhood (FSN). For multiple flexible structure comparison.

INTERNAL PAGES

fatcat.godziklab.org

1

FATCAT Flexible Structural Neighborhood(FSN) Database

http://fatcat.godziklab.org/FSN/index.html

FATCAT Flexible Structural Neighborhood(FSN) Database. Finding structural neighbors by FATCAT. For more information about FSN. Please try the server using the default PDB/SCOP ID or your own ones. SCOP169 90 NEWPDB 90. A PDB ID is a 4-charactors code for a protein assigned by Protein Data Bank. Please check PDB ID. SCOP169 90 NEWPDB 90. A SCOP domain ID(sid) is the SCOP identifier assigned by SCOP. Note: the precalculated databases only included a non-redundant list of domains. Please click on SCOP169 90.

2

FATCAT Flexible Structural Neighborhood(FSN) Database

http://fatcat.godziklab.org/fatcat/FSN/index.html

FATCAT Flexible Structural Neighborhood(FSN) Database. Finding structural neighbors by FATCAT. For more information about FSN. Please try the server using the default PDB/SCOP ID or your own ones. SCOP169 90 NEWPDB 90. A PDB ID is a 4-charactors code for a protein assigned by Protein Data Bank. Please check PDB ID. SCOP169 90 NEWPDB 90. A SCOP domain ID(sid) is the SCOP identifier assigned by SCOP. Note: the precalculated databases only included a non-redundant list of domains. Please click on SCOP169 90.

3

FATCAT references

http://fatcat.godziklab.org/reference.html

Yuzhen Ye, Adam Godzik. 2003. Flexible structure alignment by chaining aligned fragment pairs allowing twists. Bioinformatics, 19(suppl.2):ii246-ii255 PubMed. Yuzhen Ye and Adam Godzik. 2004. Database searching by flexible protein structure alignment. Protein Science, 13(7):1841-1850 PubMed. Yuzhen Ye and Adam Godzik. 2004. FATCAT: a web server for flexible structure comparison and structure similarity searching. Nucleic Acid Research, 32:W582-585 PubMed.

4

FATCAT Pairwise Alignment

http://fatcat.godziklab.org/fatcatpair.html

What does FATCAT report? See a sample report. Optional: skip it if you do not want to get results by email). Please input username/password if you would like to protect your result, otherwise leave them blank). Get the 1st structure (please use only one. Method from the 3 methods below):. Enter a name for your structure:. Upload file (in PDB format):. Provide SCOP domain code:. Get the 2nd structure (please use only one. Method from the 3 methods below):. Enter a name for your structure:.

5

FATCAT benchmarking

http://fatcat.godziklab.org/fatcatbench

This site is under construction .). Download the list of unrelated structure pairs (of length from 40 to 400) for FATCAT significance estimate:. Download the benchmark for FATCAT. Similarities between structures from different SCOP folds. 8769 pairs of structurs from different SCOP folds are analyzed( download. In 475 pairs, structural similarity was detected by FATCAT at 5% significance level( download. In 283 pairs, similarity was only detected by FATCAT( download. Go to the result page.

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posa.godziklab.org

POSA help

http://posa.godziklab.org/example.php

Sanford-Burnham Medical Research Institute. Comparison in user-guided mode by specifying one zinc finger domain in each structure. Comparison in user-guided mode by specifying one zinc finger domain in only one structure (reference). Comparison of a list of structures with 2-tandem C2H2 type zinc finger domains in automated mode. Comparison of a list of Calmodulin-like domains. Comparison of HIV virus antiboby and antigen complexes. Comparison of motifs or domains within one protein structure. Comparison...

posa.sanfordburnham.org

POSA help

http://posa.sanfordburnham.org/help.php?key=PDB

Sanford-Burnham Medical Research Institute. POSA alignment output: POA. How to read POA text file. PDB inputs in a tar/zip file. PDB inputs with user-defined constrains. POSA structure display page. How to visualize superimposed 3D structures. Tips and trouble shooting. In user-guided mode by specifying one domain in each structure. In user-guilded mode by specifying one domain in one structure(reference). NO alignments in the typical column-row format will be provided. How to read POA text file. This fi...

bioinformatics.sanfordburnham.org

Godzik Lab Website

http://bioinformatics.sanfordburnham.org/pages/servers.html

Bioinformatics and System Biology. BNAber: database of broadly neutralizing HIV antibodies. Our Institute is retiring the following domains in web and email:. Please replace them by sbpdiscovery.org. Bioinformatics Web Servers and Databases. Is a new, updated and maintained version of the F. Server is a pairwise flexible protein structure alignment server. See Bioinformatics, 2003, 19(Suppl 2):II246-II255. And Nucleic Acids Res. 2014 May 16. pii: gku394. Is a database that explores the intrinsic flexibil...

posa.sanfordburnham.org

POSA help

http://posa.sanfordburnham.org/example.php

Sanford-Burnham Medical Research Institute. Comparison in user-guided mode by specifying one zinc finger domain in each structure. Comparison in user-guided mode by specifying one zinc finger domain in only one structure (reference). Comparison of a list of structures with 2-tandem C2H2 type zinc finger domains in automated mode. Comparison of a list of Calmodulin-like domains. Comparison of HIV virus antiboby and antigen complexes. Comparison of motifs or domains within one protein structure. Comparison...

pdbflex.org

PDB Flex :: GodzikLab

http://www.pdbflex.org/index.html

The PDBFlex database explores the intrinsic flexibility of protein structures by analyzing structural variations between different depositions and chains in asymmetric unit of the same protein in PDB. It allows to easily identify regions and types of structural flexibility present in a protein of interest. Current PDB release used : Jan 17th, 2017. Enter PDB&Chain ( 1a50A. Other scientific services by our group. JS library for visualizing biological sequences. View details ». View details ».

posa.sanfordburnham.org

POSA help

http://posa.sanfordburnham.org/help.php

Sanford-Burnham Medical Research Institute. POSA alignment output: POA. How to read POA text file. PDB inputs in a tar/zip file. PDB inputs with user-defined constrains. POSA structure display page. How to visualize superimposed 3D structures. Tips and trouble shooting. In user-guided mode by specifying one domain in each structure. In user-guilded mode by specifying one domain in one structure(reference). NO alignments in the typical column-row format will be provided. How to read POA text file. This fi...

bioinformatics.sanfordburnham.org

Godzik Lab Website

http://bioinformatics.sanfordburnham.org/pages/publication.html

Bioinformatics and System Biology. BNAber: database of broadly neutralizing HIV antibodies. Our Institute is retiring the following domains in web and email:. Please replace them by sbpdiscovery.org. Porta-Pardo E, Godzik A. Mutation drivers of immunological responses to cancer. Cancer Immunol Res. 2016 Jul 11. PubMed. Thomas Hrabe, Lukasz Jaroszewski and Adam Godzik. Revealing aperiodic aspects of solenoid proteins from sequence information. Bioinformatics. 2016 Jun 9. PubMed. AIDA: ab initio domain ass...

bioinformatics.sanfordburnham.org

Godzik Lab Website

http://bioinformatics.sanfordburnham.org/pages/index.html

Bioinformatics and System Biology. BNAber: database of broadly neutralizing HIV antibodies. Our Institute is retiring the following domains in web and email:. Please replace them by sbpdiscovery.org. Physicists, biologists and computer scientists meet together to understand proteins. If you want to know more about what (and how and why) we do, read on. See our new paper. Porta-Pardo E, Godzik A., Mutation drivers of immunological responses to cancer. Cancer Immunol Res. 2016 Jul 11. A user-driven, intera...

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FATCAT - Godzik's lab

Ligned fragment pairs allowing T. Protein structures are flexible and undergo structural rearrangements as part of their function. FATCAT ( F. Ligned fragment pairs allowing T. Yuzhen Ye and Adam Godzik. Flexible structure alignment by chaining aligned fragment pairs allowing twists. 2003. Bioinformatics vol.19 suppl. 2. ii246-ii255. ( more. FATCAT Database Searching;. Flexible Structural Neighborhood (FSN). For multiple flexible structure comparison.

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