Resources:

Publications:


2016

The RCSB protein data bank: integrative view of protein, gene and 3D structural information
Nucleic Acids Research doi:10.1093/nar/gkw1000
Rose PW, Prlić A, Altunkaya A, Bi C, Bradley AR, Christie CH, Costanzo LD, Duarte JM, Dutta S, Feng Z, Green RK, Goodsell DS, Hudson B, Kalro T, Lowe R, Peisach E, Randle C, Rose AS, Shao C, Tao YP, Valasatava Y, Voigt M, Westbrook JD, Woo J, Yang H, Young JY, Zardecki C, Berman HM, Burley SK.
[article] [pubmed]


Integrating genomic information with protein sequence and 3D atomic level structure at the RCSB protein data bank
Bioinformatics, doi:10.1093/bioinformatics/btw547
A Prlić, T Kalro, R Bhattacharya, C Christie, SK Burley, PW Rose
[article] [pubmed]


2015

Detection of Circular Permutations within Protein Structures using CE-CP
Bioinformatics doi:10.1093/bioinformatics/btu823
Bliven SE, Bourne PE, Prlic A
[article] [pubmed]


2014

The RCSB Protein Data Bank: views of structural biology for basic and applied research and education
Nucleic Acids Research doi:10.1093/nar/gku1214
Rose PW, Prlić A, Bi C, Bluhm WF, Christie CH, Dutta S, Green RK, Goodsell DS, Westbrook JD, Woo J, Young J, Zardecki C, Berman HM, Bourne PE, Burley SK.
[article] [pubmed]


RCSB PDB Mobile: iOS and Android mobile apps to provide data access and visualization to the RCSB Protein Data Bank
Bioinformatics doi:10.1093/bioinformatics/btu596
Quinn GB, Bi C, Christie CH, Pang K, Prlić A, Nakane T, Zardecki C, Voigt M, Berman HM, Bourne PE, Rose PW.
[article] [pubmed]


Systematic Detection of Internal Symmetry in Proteins Using CE-Symm
Journal of Molecular Biology 426: 2255-2268 doi:10.1016/j.jmb.2014.03.010
Myers-Turnbull D1, Bliven SE2, Rose PW3, Aziz ZK4, Youkharibache P5, Bourne PE6, Prlić A7.
[article] [pubmed]


2013

Trendspotting in the Protein Data Bank.
FEBS Lett. 2013 Jan 18. pii: S0014-5793(13)00024-0. doi: 10.1016/j.febslet.2012.12.029.
Berman HM, Coimbatore Narayanan B, Costanzo LD, Dutta S, Ghosh S, Hudson BP, Lawson CL, Peisach E, Prlic A, Rose PW, Shao C, Yang H, Young J, Zardecki C.
[article] [pubmed]

The RCSB Protein Data Bank: new resources for research and education
Nucl. Acids Res. (2013) 41(D1): D475-D482 doi:10.1093/nar/gks1200
Peter W. Rose, Chunxiao Bi, Wolfgang F. Bluhm, Cole H. Christie, Dimitris Dimitropoulos, Shuchismita Dutta, Rachel K. Green, David S. Goodsell, Andreas Prlic,Martha Quesada, Gregory B. Quinn, Alexander G. Ramos, John D. Westbrook, Jasmine Young, Christine Zardecki, Helen M. Berman, and Philip E. Bourne
[abstract] [pdf] [pubmed]

2012

Ten Simple Rules for the Open Development of Scientific Software
PLoS Comput Biol 8(12): e1002802. doi:10.1371/journal.pcbi.1002802
Prlic A, Procter JB
[article] [pdf] [pubmed]

The PLOS Computational Biology Software Section
PLoS Comput Biol. 2012 Nov;8(11): e1002799. doi:10.1371/journal.pcbi.1002799
Prlic A, Lapp H
[article] [pdf] [pubmed]

BioJava: an open-source framework for bioinformatics in 2012.
Bioinformatics. 2012 Oct 15;28(20):2693-2695. Epub 2012 Aug 9.
Prlic A, Yates A, Bliven SE, Rose PW, Jacobsen J, Troshin PV, Chapman M, Gao J, Koh CH, Foisy S, Holland R, Rimsa G, Heuer ML, Brandstaetter-Mueller H, Bourne PE, Willis S.
[abstract] [pdf] [pubmed]

Circular permutation in proteins
PLoS Comput Biol 8: e1002445. 2012 Mar 29; doi:10.1371/journal.pcbi.1002445
Bliven S., Prlic A.
[abstract] [pdf] [pubmed]

2011

Quality assurance for the query and distribution systems of the RCSB Protein Data Bank.
Database (Oxford). 2011 Mar 7
Bluhm WF, Beran B, Bi C, Dimitropoulos D, Prlic A, Quinn GB, Rose PW, Shah C, Young J, Yukich B, Berman HM, Bourne PE.
[abstract] [pdf] [pubmed]

The RCSB Protein Data Bank: redesigned web site and web services.
Nucleic Acids Res. 2011 Jan;39(Databases Issue) D392-401
Rose PW, Beran B, Bi C, Bluhm WF, Dimitropoulos D, Goodsell DS, Prlic A, Quesada M, Quinn GB, Westbrook JD, Young J, Yukich B, Zardecki C, Berman HM, Bourne PE
[abstract] [pdf] [pubmed]

2010

Precalculated Protein Structure Alignments at the RCSB PDB website
Bioinformatics 2010;
Prlic A, Bliven S, Rose PW, Bluhm WF, Bizon C, Godzik A, Bourne PE
doi: 10.1093/bioinformatics/btq572
[abstract] [pdf] [pubmed]

Integration of open access literature into the RCSB Protein Data Bank Using BioLit.
BMC Bioinformatics. 2010 Apr 29;11(1):220.
Prlic A, Martinez MA, Dimitropoulos D, Beran B, Yukich BT, Rose PW, Bourne PE, Fink JL.
[abstract] [pdf] [pubmed ]

Will widgets and semantic tagging change computational biology?
PLoS Comput Biol. 2010 Feb 26;6(2)
Bourne PE, Beran B, Bi C, Bluhm W, Dunbrack R, Prlic A, Quinn G, Rose P, Shah R, Tao W, Weitzner B, Yukich B.
[abstract] [pdf] [pubmed]

2009

DASMI: exchanging, annotating and assessing molecular interaction data.
Bioinformatics. 2009 May 15;25(10):1321-8
Blankenburg H, Finn RD, Prlic A, Jenkinson AM, Ramirez F, Emig D, Schelhorn SE, Buech J, Lengauer T, Albrecht M.
[abstract] [pdf] [pubmed]

2008

The Protein Feature Ontology: A Tool for the Unification of Protein Feature Annotations
Bioinformatics. 2008 Dec 1;24(23):2767-72. Epub 2008 Oct 20
Gabrielle A. Reeves, Karen Eilbeck, Michele Magrane, Claire O'Donovan, Luisa Montecchi-Palazzi, Midori A. Harris, Sandra Orchard, Rafael C. Jimenez, Andreas Prlic, Tim J.P. Hubbard, Henning Hermjakob, and Janet M. Thornton
doi:10.1093/bioinformatics/btn528
[abstract] [pdf] [pubmed]

BioJava: an Open-Source Framework for Bioinformatics
Bioinformatics 2008 24(18):2096-2097
Richard CG Holland, Thomas A Down, Matthew Pocock, Andreas Prlic, David Huen, Keith James, Sylvain Foisy, Andreas Dräger, Andy Yates, Michael Heuer, and Mark J. Schreiber
doi:10.1093/bioinformatics/btn397
[abstract] [pdf] [pubmed]

Integrating biological data - the Distributed Annotation System
BMC Bioinformatics 2008, 9(Suppl 8):S3
Andrew M Jenkinson, Mario Albrecht, Ewan Birney, Hagen Blankenburg, Thomas Down, Robert D Finn, Henning Hermjakob, Tim JP Hubbard, Rafael C Jimenez, Philip Jones, Andreas Kahari, Eugene Kulesha, Jose R Macias, Gabrielle A Reeves, and Andreas Prlic
doi:10.1186/1471-2105-9-S8-S3
[abstract] [pdf] [pubmed]

Ensembl 2008
Nucleic Acids Res. Database Issue 2008
Flicek P, Aken BL, Beal K, Ballester B, Caccamo M, Chen Y, Clarke L, Coates G, Cunningham F, Cutts T, Down T, Dyer SC, Eyre T, Fitzgerald S, Fernandez-Banet J, Graf S, Haider S, Hammond M, Holland R, Howe KL, Howe K, Johnson N, Jenkinson A, Kahari A, Keefe D, Kokocinski F, Kulesha E, Lawson D, Longden I, Megy K, Meidl P, Overduin B, Parker A, Pritchard B, Prlic A, Rice S, Rios D, Schuster M, Sealy I, Slater G, Smedley D, Spudich G, Trevanion S, Vilella AJ, Vogel J, White S, Wood M, Birney E, Cox T, Curwen V, Durbin R, Fernandez-Suarez XM, Herrero J, Hubbard TJ, Kasprzyk A, Proctor G, Smith J, Ureta-Vidal A, Searle S.
doi:10.1093/nar/gkm988
[abstract] [pdf] [pubmed]

2007

Integrating sequence and structural biology with DAS
BMC Bioinformatics 2007, 8:333;
Andreas Prlic, Thomas A Down, Eugene Kulesha, Robert D Finn, Andreas Kahari and Tim J.P. Hubbard
[abstract] [pdf] [pubmed]

New tools and expanded data analysis capabilities at the protein structure prediction center
Proteins: Structure, Function, and Bioinformatics; 2007;69 Suppl 8:19-26.
Andriy Kryshtafovych, Andreas Prlic, Zinoviy Dmytriv, Pawel Daniluk, Maciej Milostan, Volker Eyrich, Tim Hubbard, Krzysztof Fidelis
[abstract] [pdf] [pubmed]

Ensembl 2007.
Nucleic Acids Res. Database Issue 2007
Hubbard TJ, Aken BL, Beal K, Ballester B, Caccamo M, Chen Y, Clarke L, Coates G, Cunningham F, Cutts T, Down T, Dyer SC, Fitzgerald S, Fernandez-Banet J, Graf S, Haider S, Hammond M, Herrero J, Holland R, Howe K, Howe K, Johnson N, Kahari A, Keefe D, Kokocinski F, Kulesha E, Lawson D, Longden I, Melsopp C, Megy K, Meidl P, Ouverdin B, Parker A, Prlic A, Rice S, Rios D, Schuster M, Sealy I, Severin J, Slater G, Smedley D, Spudich G, Trevanion S, Vilella A, Vogel J, White S, Wood M, Cox T, Curwen V, Durbin R, Fernandez-Suarez XM, Flicek P, Kasprzyk A, Proctor G, Searle S, Smith J, Ureta-Vidal A, Birney E.
[abstract] [pdf] [pubmed]

SISYPHUS - structural alignments for proteins with non-trivial relationships
Nucleic Acid Research Database Issue 2007 D253-D259
Antonina Andreeva, Andreas Prlic, Tim J. P. Hubbard and Alexey G. Murzin
[abstract] [pdf] [pubmed]

2006

The Distributed Annotation System for Integration of Biological Data
Data Integration in the Life Sciences: Third International Workshop, DILS 2006. Proceedings
Andreas Prlic, Ewan Birney, Tony Cox, Thomas A. Down, Rob Finn, Stefan Graef, David Jackson, Andreas Kahari, Eugene Kulesha, Roger Pettett, James Smith, Jim Stalker, Tim J. P. Hubbard
Lecture Notes in Computer Science
Publisher: Springer Berlin / Heidelberg
ISSN: 0302-9743
Volume 4075 / 2006
Editors: Ulf Leser, Felix Naumann, Barbara Eckman
ISBN: 3-540-36593-1
DOI: 10.1007/11799511
Chapter: pp. 195 - 203
[abstract] [pdf]

Ensembl 2006.
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D556-61.
Birney E, Andrews D, Caccamo M, Chen Y, Clarke L, Coates G, Cox T, Cunningham F, Curwen V, Cutts T, Down T, Durbin R, Fernandez-Suarez XM, Flicek P, Graf S, Hammond M, Herrero J, Howe K, Iyer V, Jekosch K, Kahari A, Kasprzyk A, Keefe D, Kokocinski F, Kulesha E, London D, Longden I, Melsopp C, Meidl P, Overduin B, Parker A, Proctor G, Prlic A, Rae M, Rios D, Redmond S, Schuster M, Sealy I, Searle S, Severin J, Slater G, Smedley D, Smith J, Stabenau A, Stalker J, Trevanion S, Ureta-Vidal A, Vogel J, White S, Woodwark C, Hubbard TJ.
[abstract] [pdf] [pubmed]

2005 and olders

Adding some SPICE to DAS
Bioinformatics. 2005 Volume 21, suppl_2 Pp. ii40-ii41
Prlic-A, Down-TA, Hubbard-TJP
[abstract] [pdf] [pubmed]

WILMA - platform for the annotation of protein sequences
Bioinformatics. 2004 Jan 1;20(1):127-8.
Prlic-A, Domingues-FS, Lackner-P, Sippl-MJ
[abstract] [pdf] [pubmed]

Assessment of the CASP4 Fold Recognition Category.
Proteins. 2001; 45 (S5): 55-67
Sippl-MJ, Lackner-P, Domingues-FS, Prlic-A, Malik-R, Andreeva-A, Wiederstein-M [abstract] [pdf] [pubmed]

Structure-derived substitution matrices for alignment of distantly related sequences.
Protein Eng. 2000 Aug;13(8):545-50
Prlic-A, Domingues-FS, Sippl-MJ
[abstract] [pdf] [pubmed]

Sustained performance of knowledge-based potentials in fold recognition.
Proteins. 1999;37(S3):112-20
Domingues-FS, Koppensteiner-WA, Jaritz-M, Prlic-A, Weichenberger-C, Wiederstein-M, Floeckner-H, Lackner-P, Sippl-MJ
[abstract] [pdf] [pubmed]