Literature DB >> 18641403

PIGS: automatic prediction of antibody structures.

Paolo Marcatili1, Alessandra Rosi, Anna Tramontano.   

Abstract

UNLABELLED: We describe a web server for the automatic prediction of immunoglobulin variable domains based on the canonical structure model. The server is user-friendly and flexible. It allows the user to select the templates for the frameworks and the loops using different strategies. The final output is a full-fledged 3D model of the variable domains of the target immunoglobulin. AVAILABILITY: The server is openly accessible to academic users at the address: http://arianna.bio.uniroma1.it/pigs. It does not require registration and there is no limit to the number of sequences that can be submitted.

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Year:  2008        PMID: 18641403     DOI: 10.1093/bioinformatics/btn341

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


  83 in total

1.  Stereotyped patterns of B-cell receptor in splenic marginal zone lymphoma.

Authors:  Silvia Zibellini; Daniela Capello; Francesco Forconi; Paolo Marcatili; Davide Rossi; Sara Rattotti; Silvia Franceschetti; Elisa Sozzi; Emanuele Cencini; Roberto Marasca; Luca Baldini; Alessandra Tucci; Francesco Bertoni; Francesco Passamonti; Ester Orlandi; Marzia Varettoni; Michele Merli; Silvia Rizzi; Valter Gattei; Anna Tramontano; Marco Paulli; Gianluca Gaidano; Luca Arcaini
Journal:  Haematologica       Date:  2010-05-29       Impact factor: 9.941

2.  Constitutive production of catalytic antibodies to a Staphylococcus aureus virulence factor and effect of infection.

Authors:  Eric L Brown; Yasuhiro Nishiyama; Jesse W Dunkle; Shreya Aggarwal; Stephanie Planque; Kenji Watanabe; Keri Csencsits-Smith; M Gabriela Bowden; Sheldon L Kaplan; Sudhir Paul
Journal:  J Biol Chem       Date:  2012-02-02       Impact factor: 5.157

3.  Antibody humanization by structure-based computational protein design.

Authors:  Yoonjoo Choi; Casey Hua; Charles L Sentman; Margaret E Ackerman; Chris Bailey-Kellogg
Journal:  MAbs       Date:  2015-08-07       Impact factor: 5.857

4.  A new clustering of antibody CDR loop conformations.

Authors:  Benjamin North; Andreas Lehmann; Roland L Dunbrack
Journal:  J Mol Biol       Date:  2010-10-28       Impact factor: 5.469

5.  Using homology modeling to interrogate binding affinity in neutralization of ricin toxin by a family of single domain antibodies.

Authors:  Andrea Bazzoli; David J Vance; Michael J Rudolph; Yinghui Rong; Siva Krishna Angalakurthi; Ronald T Toth; C Russell Middaugh; David B Volkin; David D Weis; John Karanicolas; Nicholas J Mantis
Journal:  Proteins       Date:  2017-08-04

6.  Antibody modeling using the prediction of immunoglobulin structure (PIGS) web server [corrected].

Authors:  Paolo Marcatili; Pier Paolo Olimpieri; Anna Chailyan; Anna Tramontano
Journal:  Nat Protoc       Date:  2014-11-06       Impact factor: 13.491

7.  AbRSA: A robust tool for antibody numbering.

Authors:  Lei Li; Shuang Chen; Zhichao Miao; Yang Liu; Xu Liu; Zhi-Xiong Xiao; Yang Cao
Journal:  Protein Sci       Date:  2019-05-11       Impact factor: 6.725

8.  Structural basis of a potent human monoclonal antibody against Zika virus targeting a quaternary epitope.

Authors:  Feng Long; Michael Doyle; Estefania Fernandez; Andrew S Miller; Thomas Klose; Madhumati Sevvana; Aubrey Bryan; Edgar Davidson; Benjamin J Doranz; Richard J Kuhn; Michael S Diamond; James E Crowe; Michael G Rossmann
Journal:  Proc Natl Acad Sci U S A       Date:  2019-01-14       Impact factor: 11.205

9.  Broadly neutralizing epitopes in the Plasmodium vivax vaccine candidate Duffy Binding Protein.

Authors:  Edwin Chen; Nichole D Salinas; Yining Huang; Francis Ntumngia; Manolo D Plasencia; Michael L Gross; John H Adams; Niraj Harish Tolia
Journal:  Proc Natl Acad Sci U S A       Date:  2016-05-18       Impact factor: 11.205

10.  RosettaAntibody: antibody variable region homology modeling server.

Authors:  Aroop Sircar; Eric T Kim; Jeffrey J Gray
Journal:  Nucleic Acids Res       Date:  2009-05-20       Impact factor: 16.971

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