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References:
2023
Development and application of a computable genotype model in the GA4GH Variation Representation SpecificationPacific Symposium on Biocomputing, 28:383–394
Wesley Goar, Lawrence Babb, Srikar Chamala, Melissa Cline, Robert R Freimuth, Reece K Hart, Kori Kuzma, Jennifer Lee, Tristan Nelson, Andreas Prlić, Kevin Riehle, Anastasia Smith, Kathryn Stahl, Andrew David Yates, Heidi L Rehm, Alex H Wagner
[pdf] [pubmed]2021
GA4GH: International policies and standards for data sharing across genomic research and healthcareCell Genomics 1(2):100029
[article] [pubmed]
2020
SeqRepo: A system for managing local collections of biological sequencesPLoS ONE 15(12):e0239883
RK Hart, A Prlić
[article] [pdf] [pubmed]
2019
BioJava 5: A community driven open-source bioinformatics libraryPLoS Computational Biology
Aleix Lafita, Spencer Bliven, Andreas Prlić, Dmytro Guzenko, Peter W Rose, Anthony Bradley, Paolo Pavan, Douglas Myers-Turnbull, Yana Valasatava, Michael Heuer, Matt Larson, Stephen K Burley, Jose M Duarte
[article] [pdf] [pubmed]
RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy
Nucleic Acids Research
Stephen K Burley, Helen M Berman, Charmi Bhikadiya, Chunxiao Bi, Li Chen, Luigi Di Costanzo, Cole Christie, Ken Dalenberg, Jose M Duarte, Shuchismita Dutta, Zukang Feng, Sutapa Ghosh, David S Goodsell, Rachel K Green, Vladimir Guranovic, Dmytro Guzenko, Brian P Hudson, Tara Kalro, Yuhe Liang, Robert Lowe, Harry Namkoong, Ezra Peisach, Irina Periskova, Andreas Prlić, Chris Randle, Alexander Rose, Peter Rose, Raul Sala, Monica Sekharan, Chenghua Shao, Lihua Tan, Yi-Ping Tao, Yana Valasatava, Maria Voigt, John Westbrook, Jesse Woo, Huanwang Yang, Jasmine Young, Marina Zhuravleva, Christine Zardecki
[article] [pubmed]
Analyzing the symmetrical arrangement of structural repeats in proteins with CE-Symm
PLoS Computational Biology
Spencer E Bliven, Aleix Lafita, Peter W Rose, Guido Capitani, Andreas Prlić, Philip E Bourne
[article] [pdf] [pubmed]
2018
hgvs: a Python package for manipulating sequence variants using HGVS nomenclature: 2018 updateHuman Mutation
Meng Wang, Keith M Callenberg, Raymond Dalgleish, Alexandre Fedtsov, Naomi K Fox, Peter J Freeman, Kevin B Jacobs, Piotr Kaleta, Andrew J McMurry, Andreas Prlić, Veena Rajaraman, Reece K Hart
[article] [pubmed]
Investigation of protein quaternary structure via stoichiometry and symmetry information
PLoS ONE 13(6):e0197176
Selcuk Korkmaz, Jose M Duarte, Andreas Prlić, Dincer Goksuluk, Gokmen Zararsiz, Osman Saracbasi, Stephen K Burley, Peter W Rose
[article] [pdf] [pubmed]
Recon3D enables a three-dimensional view of gene variation in human metabolism
Nature Biotechnology
Elizabeth Brunk, Swagatika Sahoo, Daniel C Zielinski, Ali Altunkaya, Andreas Drager, Nathan Mih, Francesco Gatto, Avlant Nilsson, German Andres Preciat Gonzalez, Maike Kathrin Aurich, Andreas Prlić, Anand Sastry, Anna D Danielsdottir, Almut Heinken, Alberto Noronha, Peter W Rose, Stephen K Burley, Ronan MT Fleming, Jens Nielsen, Ines Thiele, Bernhard O Palsson
[article] [pubmed]
2017
Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed frameworkGenome Medicine
Gustavo Glusman, Peter W Rose, Andreas Prlić, Jennifer Dougherty, Jose M Duarte, Andrew S Hoffman, Geoffrey J Barton, Emoke Bendixen, Timothy Bergquist, Christian Bock, Elizabeth Brunk, Marija Buljan, Stephen K Burley, Binghuang Cai, Hannah Carter, JianJiong Gao, Adam Godzik, Michael Heuer, Michael Hicks, Thomas Hrabe, Rachel Karchin, Julia Koehler Leman, Lydie Lane, David L Masica, Sean D Mooney, John Moult, Gilbert S Omenn, Frances Pearl, Vikas Pejaver, Sheila M Reynolds, Ariel Rokem, Torsten Schwede, Sicheng Song, Hagen Tilgner, Yana Valasatava, Yang Zhang, Eric W Deutsch
[article] [pdf] [pubmed]
Impact of genetic variation on three dimensional structure and function of proteins
PLoS ONE
Roshni Bhattacharya, Peter W Rose, Stephen K Burley, Andreas Prlić
[article] [pdf] [pubmed]
2016
The RCSB protein data bank: integrative view of protein, gene and 3D structural informationNucleic 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]
Bioinformatics, doi:10.1093/bioinformatics/btw547
A Prlić, T Kalro, R Bhattacharya, C Christie, SK Burley, PW Rose
[article] [pubmed]
2015
The Protein Data Bank: overview and tools for drug discoveryMultifaceted Roles of Crystallography in Modern Drug Discovery (book chapter)
Berman HM, Rose PW, Dutta S, Zardecki C, Prlić A
[article]
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 educationNucleic 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]
</li>
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 SoftwarePLoS 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
The evolution of the RCSB Protein Data Bank websiteWIREs Computational Molecular Science, 1(5):782–789
Bourne PE, Beran B, Bi C, Bluhm WF, Dimitropoulos D, Feng Z, Goodsell DS, Prlić A, Quinn GB, Rose PW, et al.
[article] [pubmed]
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 websiteBioinformatics 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 AnnotationsBioinformatics. 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 DASBMC 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 DataData 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 earlier
Adding some SPICE to DASBioinformatics. 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]