Literature DB >> 15215345

3DCoffee@igs: a web server for combining sequences and structures into a multiple sequence alignment.

Olivier Poirot1, Karsten Suhre, Chantal Abergel, Eamonn O'Toole, Cedric Notredame.   

Abstract

This paper presents 3DCoffee@igs, a web-based tool dedicated to the computation of high-quality multiple sequence alignments (MSAs). 3D-Coffee makes it possible to mix protein sequences and structures in order to increase the accuracy of the alignments. Structures can be either provided as PDB identifiers or directly uploaded into the server. Given a set of sequences and structures, pairs of structures are aligned with SAP while sequence-structure pairs are aligned with Fugue. The resulting collection of pairwise alignments is then combined into an MSA with the T-Coffee algorithm. The server and its documentation are available from http://igs-server.cnrs-mrs.fr/Tcoffee/.

Entities:  

Mesh：

Substances：

Year:  2004        PMID： 15215345      PMCID： PMC441520          DOI： 10.1093/nar/gkh382

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN： 0305-1048            Impact factor:   16.971


  17 in total

1.  Protein secondary structure prediction based on position-specific scoring matrices.

Authors:  D T Jones
Journal:  J Mol Biol       Date:  1999-09-17       Impact factor: 5.469

2.  HOMSTRAD: adding sequence information to structure-based alignments of homologous protein families.

Authors:  P I de Bakker; A Bateman; D F Burke; R N Miguel; K Mizuguchi; J Shi; H Shirai; T L Blundell
Journal:  Bioinformatics       Date:  2001-08       Impact factor: 6.937

3.  FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties.

Authors:  J Shi; T L Blundell; K Mizuguchi
Journal:  J Mol Biol       Date:  2001-06-29       Impact factor: 5.469

4.  Accounting for human polymorphisms predicted to affect protein function.

Authors:  Pauline C Ng; Steven Henikoff
Journal:  Genome Res       Date:  2002-03       Impact factor: 9.043

5.  T-Coffee: A novel method for fast and accurate multiple sequence alignment.

Authors:  C Notredame; D G Higgins; J Heringa
Journal:  J Mol Biol       Date:  2000-09-08       Impact factor: 5.469

6.  The InterPro Database, 2003 brings increased coverage and new features.

Authors:  Nicola J Mulder; Rolf Apweiler; Teresa K Attwood; Amos Bairoch; Daniel Barrell; Alex Bateman; David Binns; Margaret Biswas; Paul Bradley; Peer Bork; Phillip Bucher; Richard R Copley; Emmanuel Courcelle; Ujjwal Das; Richard Durbin; Laurent Falquet; Wolfgang Fleischmann; Sam Griffiths-Jones; Daniel Haft; Nicola Harte; Nicolas Hulo; Daniel Kahn; Alexander Kanapin; Maria Krestyaninova; Rodrigo Lopez; Ivica Letunic; David Lonsdale; Ville Silventoinen; Sandra E Orchard; Marco Pagni; David Peyruc; Chris P Ponting; Jeremy D Selengut; Florence Servant; Christian J A Sigrist; Robert Vaughan; Evgueni M Zdobnov
Journal:  Nucleic Acids Res       Date:  2003-01-01       Impact factor: 16.971

7.  Tcoffee@igs: A web server for computing, evaluating and combining multiple sequence alignments.

Authors:  Olivier Poirot; Eamonn O'Toole; Cedric Notredame
Journal:  Nucleic Acids Res       Date:  2003-07-01       Impact factor: 16.971

8.  ESPript/ENDscript: Extracting and rendering sequence and 3D information from atomic structures of proteins.

Authors:  Patrice Gouet; Xavier Robert; Emmanuel Courcelle
Journal:  Nucleic Acids Res       Date:  2003-07-01       Impact factor: 16.971

9.  APDB: a novel measure for benchmarking sequence alignment methods without reference alignments.

Authors:  Orla O'Sullivan; Mark Zehnder; Des Higgins; Philipp Bucher; Aurelien Grosdidier; Cédric Notredame
Journal:  Bioinformatics       Date:  2003       Impact factor: 6.937

10.  Human non-synonymous SNPs: server and survey.

Authors:  Vasily Ramensky; Peer Bork; Shamil Sunyaev
Journal:  Nucleic Acids Res       Date:  2002-09-01       Impact factor: 16.971
View more
  68 in total

1.  MSACompro: protein multiple sequence alignment using predicted secondary structure, solvent accessibility, and residue-residue contacts.

Authors:  Xin Deng; Jianlin Cheng
Journal:  BMC Bioinformatics       Date:  2011-12-14       Impact factor: 3.169

2.  Midkine and pleiotrophin have bactericidal properties: preserved antibacterial activity in a family of heparin-binding growth factors during evolution.

Authors:  Sara L Svensson; Mukesh Pasupuleti; Björn Walse; Martin Malmsten; Matthias Mörgelin; Camilla Sjögren; Anders I Olin; Mattias Collin; Artur Schmidtchen; Ruth Palmer; Arne Egesten
Journal:  J Biol Chem       Date:  2010-03-22       Impact factor: 5.157

3.  Gene and genome duplication in Acanthamoeba polyphaga Mimivirus.

Authors:  Karsten Suhre
Journal:  J Virol       Date:  2005-11       Impact factor: 5.103

4.  Solution structure of APETx2, a specific peptide inhibitor of ASIC3 proton-gated channels.

Authors:  Benjamin Chagot; Pierre Escoubas; Sylvie Diochot; Cédric Bernard; Michel Lazdunski; Hervé Darbon
Journal:  Protein Sci       Date:  2005-06-29       Impact factor: 6.725

5.  Structure of the B3 domain from Arabidopsis thaliana protein At1g16640.

Authors:  Jeanette K Waltner; Francis C Peterson; Betsy L Lytle; Brian F Volkman
Journal:  Protein Sci       Date:  2005-08-04       Impact factor: 6.725

6.  Gene cooption without duplication during the evolution of a male-pregnancy gene in pipefish.

Authors:  April Harlin-Cognato; Eric A Hoffman; Adam G Jones
Journal:  Proc Natl Acad Sci U S A       Date:  2006-12-08       Impact factor: 11.205

7.  Identification and characterization of RsmE, the founding member of a new RNA base methyltransferase family.

Authors:  Georgeta N Basturea; Kenneth E Rudd; Murray P Deutscher
Journal:  RNA       Date:  2006-01-23       Impact factor: 4.942

8.  Mimivirus TyrRS: preliminary structural and functional characterization of the first amino-acyl tRNA synthetase found in a virus.

Authors:  Chantal Abergel; Sabine Chenivesse; Deborah Byrne; Karsten Suhre; Vincent Arondel; Jean-Michel Claverie
Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun       Date:  2005-01-20

9.  Acanthamoeba polyphaga mimivirus NDK: preliminary crystallographic analysis of the first viral nucleoside diphosphate kinase.

Authors:  Sandra Jeudy; Bruno Coutard; Régine Lebrun; Chantal Abergel
Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun       Date:  2005-06-01

10.  Recognition of a complex substrate by the KsgA/Dim1 family of enzymes has been conserved throughout evolution.

Authors:  Heather C O'Farrell; Nagesh Pulicherla; Pooja M Desai; Jason P Rife
Journal:  RNA       Date:  2006-03-15       Impact factor: 4.942
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.