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Bioinformatics Web Servers & Databases

FFAS is a new, updated and maintained version of the Fold & Function Assignment System. The FFAS fold assignment method is based on the profile-profile matching algorithm. The crucial part of the algorithm is the novel, two dimensional weighting scheme which takes into account the topology of the evolutionary tree of all the proteins in the homologous family. Please see References for details.
FATCAT server is a pairwise flexible protein structure alignment server. See Bioinformatics, 2003, 19(Suppl 2):II246-II255 for details.
POSA server is a multiple flexible protein structure alignment server. See Bioinformatics, 2005 21(10):2362-2369 and Nucleic Acids Res. 2014 May 16. pii: gku394. for details.
Cancer3D is a database that puts together information on somatic missense mutations from TCGA and CCLE, allowing users to explore two different cancer-related problems at the same time: drug sensitivity/biomarker identification and prediction of cancer drivers. Please see Nucl. Acids Res. (2014) for details.
PDBflex is a database that 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. Please see Nucl. Acids Res. (2015) doi: 10.1093/nar/gkv1316 for details.
AIDA: ab initio domain assembly server, available at http://aida.godziklab.org is a tool that can identify domains in multi-domain proteins and then predict their 3D structures and relative spatial arrangements. Please see Nucl. Acids Res. (1 July 2014) 42 (W1): W308-W313. for details.
Protael, available at http://protael.org/, is a JS library for visualizing biological sequences. Please see Bioinformatics (2015) doi: 10.1093/bioinformatics/btv605 for details.
PubServer, available at http://pubserver.godziklab.org/, is a tool to automatically collect, filter and analyze publications associated with groups of homologous proteins. Please see Nucl. Acids Res. (1 July 2014) 42 (W1): W430-W435. doi: 10.1093/nar/gku450 for details.
XtalPred server is a server to predict protein crystallizability. Please see Bioinformatics, 2007 23(24):3403-5 for server information and see Acta Crystallogr D Biol Crystallogr. 2014 for method details.
bNAber is a database of broadly neutralizing HIV antibodies. Please see Nucl. Acids Res. (1 January 2014) 42 (D1): D1133-D1139. doi: 10.1093/nar/gkt1083 for details.
ConSole is server to use modularity of contact maps to locate solenoid domains in protein structures. Please see BMC Bioinformatics. 2014 Apr 27;15:119. doi: 10.1186/1471-2105-15-119 for details.
ProtMod is a protein modeling server. Its task is to predicts 3-dimensional structures of proteins based on their sequences. Instead of generating only one model for a given protein, ProtMod produces a list of protein models and orders them by different model evaluation scores.

Web Servers that Are no longer Maintained

CADO is server for Comparative Analysis of protein Domain Organization. A graph theory method to survey and compare domain organization across genomes. Described in Genome Research, 2004, 14:343-353
TOPS++FATCAT uses TOPS to limit the search space of the aligned fragment pairs (AFPs) in the flexible alignment of protein structures performed by the FATCAT algorithm. Such intuitions could help speed up similarity searches and make it easier to understand the results of such analyses. See BMC Bioinformatics, 9:358, 2008. for details.
SEA is a novel approach to protein sequence alignment, the structure SEgment Alignment server. It is based on the network mathcing approach, and profile-profile comparison of short fragments of sequence. See Bioinformatics, 2003, 19:742-9 for details.
FRAGlib is server that predicts local structure segments in proteins by the profile-profile matching algorithm based on the database of short (7-19aa) secondary structural motifs chosen from ASTRAL SCOP database.
Wikiomics is a wiki for the bioinformatics community that is hosted on one of our servers. The principle is to reduce the communication barriers between scientists, by letting anyone instantly edit, review, update and discuss any part of the web site. Hosted under an independent domain name, we are confident Wikiomics will become a tool of choice for every modern scientist concerned with bioinformatics.