Literature DB >> 17237055

SMotif: a server for structural motifs in proteins.

Ganesan Pugalenthi1, P N Suganthan, R Sowdhamini, Saikat Chakrabarti.   

Abstract

UNLABELLED: SMotif is a server that identifies important structural segments or motifs for a given protein structure(s) based on conservation of both sequential as well as important structural features such as solvent inaccessibility, secondary structural content, hydrogen bonding pattern and residue packing. This server also provides three-dimensional orientation patterns of the identified motifs in terms of inter-motif distances and torsion angles. These motifs may form the common core and therefore, can also be employed to design and rationalize protein engineering and folding experiments. AVAILABILITY: SMotif server is available via the URL http://caps.ncbs.res.in/SMotif/index.html. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

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Year:  2007        PMID： 17237055     DOI： 10.1093/bioinformatics/btl679

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  9 in total

Review 1.  Interpreting functional effects of coding variants: challenges in proteome-scale prediction, annotation and assessment.

Authors:  Khader Shameer; Lokesh P Tripathi; Krishna R Kalari; Joel T Dudley; Ramanathan Sowdhamini
Journal:  Brief Bioinform       Date:  2015-10-22       Impact factor: 11.622

2.  PASS2 version 4: an update to the database of structure-based sequence alignments of structural domain superfamilies.

Authors:  A Gandhimathi; Anu G Nair; R Sowdhamini
Journal:  Nucleic Acids Res       Date:  2011-11-28       Impact factor: 16.971

3.  PASS2.7: a database containing structure-based sequence alignments and associated features of protein domain superfamilies from SCOPe.

Authors:  Teerna Bhattacharyya; Soumya Nayak; Smit Goswami; Vasundhara Gadiyaram; Oommen K Mathew; Ramanathan Sowdhamini
Journal:  Database (Oxford)       Date:  2022-04-12       Impact factor: 4.462

4.  MegaMotifBase: a database of structural motifs in protein families and superfamilies.

Authors:  Ganesan Pugalenthi; P N Suganthan; R Sowdhamini; Saikat Chakrabarti
Journal:  Nucleic Acids Res       Date:  2007-10-11       Impact factor: 16.971

5.  PASS2 version 6: a database of structure-based sequence alignments of protein domain superfamilies in accordance with SCOPe.

Authors:  Pritha Ghosh; Teerna Bhattacharyya; Oommen K Mathew; Ramanathan Sowdhamini
Journal:  Database (Oxford)       Date:  2019-01-01       Impact factor: 3.451

6.  Probing ion channel functional architecture and domain recombination compatibility by massively parallel domain insertion profiling.

Authors:  Willow Coyote-Maestas; David Nedrud; Antonio Suma; Yungui He; Kenneth A Matreyek; Douglas M Fowler; Vincenzo Carnevale; Chad L Myers; Daniel Schmidt
Journal:  Nat Commun       Date:  2021-12-08       Impact factor: 14.919

7.  Identification of structurally conserved residues of proteins in absence of structural homologs using neural network ensemble.

Authors:  Ganesan Pugalenthi; Ke Tang; P N Suganthan; Saikat Chakrabarti
Journal:  Bioinformatics       Date:  2008-11-27       Impact factor: 6.937

8.  ECMIS: computational approach for the identification of hotspots at protein-protein interfaces.

Authors:  Prashant Shingate; Malini Manoharan; Anshul Sukhwal; Ramanathan Sowdhamini
Journal:  BMC Bioinformatics       Date:  2014-09-16       Impact factor: 3.169

9.  PASS2 database for the structure-based sequence alignment of distantly related SCOP domain superfamilies: update to version 5 and added features.

Authors:  Arumugam Gandhimathi; Pritha Ghosh; Sridhar Hariharaputran; Oommen K Mathew; R Sowdhamini
Journal:  Nucleic Acids Res       Date:  2015-11-08       Impact factor: 16.971
  9 in total

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