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Andreas Prlic

SchoolVc-academic Affairs
Address9500 Gilman Drive #0505
La Jolla CA 92093
Phone8/2-46--0526
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Analyzing the symmetrical arrangement of structural repeats in proteins with CE-Symm. PLoS Comput Biol. 2019 04; 15(4):e1006842. Bliven SE, Lafita A, Rose PW, Capitani G, Prlic A, Bourne PE. PMID: 31009453.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    2. BioJava 5: A community driven open-source bioinformatics library. PLoS Comput Biol. 2019 02; 15(2):e1006791. Lafita A, Bliven S, Prlic A, Guzenko D, Rose PW, Bradley A, Pavan P, Myers-Turnbull D, Valasatava Y, Heuer M, Larson M, Burley SK, Duarte JM. PMID: 30735498.
      View in: PubMed   Mentions: 2     Fields:    
    3. RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy. Nucleic Acids Res. 2019 01 08; 47(D1):D464-D474. Burley SK, Berman HM, Bhikadiya C, Bi C, Chen L, Di Costanzo L, Christie C, Dalenberg K, Duarte JM, Dutta S, Feng Z, Ghosh S, Goodsell DS, Green RK, Guranovic V, Guzenko D, Hudson BP, Kalro T, Liang Y, Lowe R, Namkoong H, Peisach E, Periskova I, Prlic A, Randle C, Rose A, Rose P, Sala R, Sekharan M, Shao C, Tan L, Tao YP, Valasatava Y, Voigt M, Westbrook J, Woo J, Yang H, Young J, Zhuravleva M, Zardecki C. PMID: 30357411.
      View in: PubMed   Mentions: 66     Fields:    Translation:Cells
    4. NGL viewer: web-based molecular graphics for large complexes. Bioinformatics. 2018 11 01; 34(21):3755-3758. Rose AS, Bradley AR, Valasatava Y, Duarte JM, Prlic A, Rose PW. PMID: 29850778.
      View in: PubMed   Mentions: 49     Fields:    
    5. hgvs: A Python package for manipulating sequence variants using HGVS nomenclature: 2018 Update. Hum Mutat. 2018 12; 39(12):1803-1813. Wang M, Callenberg KM, Dalgleish R, Fedtsov A, Fox NK, Freeman PJ, Jacobs KB, Kaleta P, McMurry AJ, Prlic A, Rajaraman V, Hart RK. PMID: 30129167.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    6. Investigation of protein quaternary structure via stoichiometry and symmetry information. PLoS One. 2018; 13(6):e0197176. Korkmaz S, Duarte JM, Prlic A, Goksuluk D, Zararsiz G, Saracbasi O, Burley SK, Rose PW. PMID: 29864163.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    7. Recon3D enables a three-dimensional view of gene variation in human metabolism. Nat Biotechnol. 2018 03; 36(3):272-281. Brunk E, Sahoo S, Zielinski DC, Altunkaya A, Dräger A, Mih N, Gatto F, Nilsson A, Preciat Gonzalez GA, Aurich MK, Prlic A, Sastry A, Danielsdottir AD, Heinken A, Noronha A, Rose PW, Burley SK, Fleming RMT, Nielsen J, Thiele I, Palsson BO. PMID: 29457794.
      View in: PubMed   Mentions: 33     Fields:    Translation:Humans
    8. Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework. Genome Med. 2017 Dec 18; 9(1):113. Glusman G, Rose PW, Prlic A, Dougherty J, Duarte JM, Hoffman AS, Barton GJ, Bendixen E, Bergquist T, Bock C, Brunk E, Buljan M, Burley SK, Cai B, Carter H, Gao J, Godzik A, Heuer M, Hicks M, Hrabe T, Karchin R, Leman JK, Lane L, Masica DL, Mooney SD, Moult J, Omenn GS, Pearl F, Pejaver V, Reynolds SM, Rokem A, Schwede T, Song S, Tilgner H, Valasatava Y, Zhang Y, Deutsch EW. PMID: 29254494.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansCells
    9. BioJava-ModFinder: identification of protein modifications in 3D structures from the Protein Data Bank. Bioinformatics. 2017 Jul 01; 33(13):2047-2049. Gao J, Prlic A, Bi C, Bluhm WF, Dimitropoulos D, Xu D, Bourne PE, Rose PW. PMID: 28334105.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    10. MMTF-An efficient file format for the transmission, visualization, and analysis of macromolecular structures. PLoS Comput Biol. 2017 Jun; 13(6):e1005575. Bradley AR, Rose AS, Pavelka A, Valasatava Y, Duarte JM, Prlic A, Rose PW. PMID: 28574982.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    11. Towards an efficient compression of 3D coordinates of macromolecular structures. PLoS One. 2017; 12(3):e0174846. Valasatava Y, Bradley AR, Rose AS, Duarte JM, Prlic A, Rose PW. PMID: 28362865.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    12. Impact of genetic variation on three dimensional structure and function of proteins. PLoS One. 2017; 12(3):e0171355. Bhattacharya R, Rose PW, Burley SK, Prlic A. PMID: 28296894.
      View in: PubMed   Mentions: 3     Fields:    
    13. The RCSB protein data bank: integrative view of protein, gene and 3D structural information. Nucleic Acids Res. 2017 01 04; 45(D1):D271-D281. Rose PW, Prlic 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. PMID: 27794042.
      View in: PubMed   Mentions: 130     Fields:    Translation:Cells
    14. Integrating genomic information with protein sequence and 3D atomic level structure at the RCSB protein data bank. Bioinformatics. 2016 12 15; 32(24):3833-3835. Prlic A, Kalro T, Bhattacharya R, Christie C, Burley SK, Rose PW. PMID: 27551105.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansCells
    15. Detection of circular permutations within protein structures using CE-CP. Bioinformatics. 2015 Apr 15; 31(8):1316-8. Bliven SE, Bourne PE, Prlic A. PMID: 25505094.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    16. The RCSB Protein Data Bank: views of structural biology for basic and applied research and education. Nucleic Acids Res. 2015 Jan; 43(Database issue):D345-56. Rose PW, Prlic 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. PMID: 25428375.
      View in: PubMed   Mentions: 166     Fields:    Translation:Cells
    17. RCSB PDB Mobile: iOS and Android mobile apps to provide data access and visualization to the RCSB Protein Data Bank. Bioinformatics. 2015 Jan 01; 31(1):126-7. Quinn GB, Bi C, Christie CH, Pang K, Prlic A, Nakane T, Zardecki C, Voigt M, Berman HM, Bourne PE, Rose PW. PMID: 25183487.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    18. Systematic detection of internal symmetry in proteins using CE-Symm. J Mol Biol. 2014 May 29; 426(11):2255-68. Myers-Turnbull D, Bliven SE, Rose PW, Aziz ZK, Youkharibache P, Bourne PE, Prlic A. PMID: 24681267.
      View in: PubMed   Mentions: 15     Fields:    Translation:HumansCells
    19. Trendspotting in the Protein Data Bank. FEBS Lett. 2013 Apr 17; 587(8):1036-45. Berman HM, Coimbatore Narayanan B, Di Costanzo L, Dutta S, Ghosh S, Hudson BP, Lawson CL, Peisach E, Prlic A, Rose PW, Shao C, Yang H, Young J, Zardecki C. PMID: 23337870.
      View in: PubMed   Mentions: 33     Fields:    Translation:Cells
    20. Ten simple rules for the open development of scientific software. PLoS Comput Biol. 2012; 8(12):e1002802. Prlic A, Procter JB. PMID: 23236269.
      View in: PubMed   Mentions: 33     Fields:    
    21. The RCSB Protein Data Bank: new resources for research and education. Nucleic Acids Res. 2013 Jan; 41(Database issue):D475-82. Rose PW, Bi C, Bluhm WF, Christie CH, Dimitropoulos D, Dutta S, Green RK, Goodsell DS, Prlic A, Quesada M, Quinn GB, Ramos AG, Westbrook JD, Young J, Zardecki C, Berman HM, Bourne PE. PMID: 23193259.
      View in: PubMed   Mentions: 172     Fields:    Translation:Cells
    22. BioJava: an open-source framework for bioinformatics in 2012. Bioinformatics. 2012 Oct 15; 28(20):2693-5. 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, Brandstätter-Müller H, Bourne PE, Willis S. PMID: 22877863.
      View in: PubMed   Mentions: 61     Fields:    Translation:Cells
    23. Circular permutation in proteins. PLoS Comput Biol. 2012; 8(3):e1002445. Bliven S, Prlic A. PMID: 22496628.
      View in: PubMed   Mentions: 11     Fields:    Translation:Cells
    24. Quality assurance for the query and distribution systems of the RCSB Protein Data Bank. Database (Oxford). 2011; 2011:bar003. Bluhm WF, Beran B, Bi C, Dimitropoulos D, Prlic A, Quinn GB, Rose PW, Shah C, Young J, Yukich B, Berman HM, Bourne PE. PMID: 21382834.
      View in: PubMed   Mentions: 3     Fields:    
    25. The RCSB Protein Data Bank: redesigned web site and web services. Nucleic Acids Res. 2011 Jan; 39(Database 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. PMID: 21036868.
      View in: PubMed   Mentions: 222     Fields:    Translation:HumansAnimalsCells
    26. Pre-calculated protein structure alignments at the RCSB PDB website. Bioinformatics. 2010 Dec 01; 26(23):2983-5. Prlic A, Bliven S, Rose PW, Bluhm WF, Bizon C, Godzik A, Bourne PE. PMID: 20937596.
      View in: PubMed   Mentions: 69     Fields:    Translation:Cells
    27. Integration of open access literature into the RCSB Protein Data Bank using BioLit. BMC Bioinformatics. 2010 Apr 29; 11:220. Prlic A, Martinez MA, Dimitropoulos D, Beran B, Yukich BT, Rose PW, Bourne PE, Fink JL. PMID: 20429930.
      View in: PubMed   Mentions: 5     Fields:    
    28. Will widgets and semantic tagging change computational biology? PLoS Comput Biol. 2010 Feb 26; 6(2):e1000673. Bourne PE, Beran B, Bi C, Bluhm W, Dunbrack R, Prlic A, Quinn G, Rose P, Shah R, Tao W, Weitzner B, Yukich B. PMID: 20195550.
      View in: PubMed   Mentions: 4     Fields:    
    29. DASMI: exchanging, annotating and assessing molecular interaction data. Bioinformatics. 2009 May 15; 25(10):1321-8. Blankenburg H, Finn RD, Prlic A, Jenkinson AM, Ramírez F, Emig D, Schelhorn SE, Büch J, Lengauer T, Albrecht M. PMID: 19420069.
      View in: PubMed   Mentions: 5     Fields:    
    30. The Protein Feature Ontology: a tool for the unification of protein feature annotations. Bioinformatics. 2008 Dec 01; 24(23):2767-72. Reeves GA, Eilbeck K, Magrane M, O'Donovan C, Montecchi-Palazzi L, Harris MA, Orchard S, Jimenez RC, Prlic A, Hubbard TJ, Hermjakob H, Thornton JM. PMID: 18936051.
      View in: PubMed   Mentions: 9     Fields:    
    31. Integrating biological data--the Distributed Annotation System. BMC Bioinformatics. 2008 Jul 22; 9 Suppl 8:S3. Jenkinson AM, Albrecht M, Birney E, Blankenburg H, Down T, Finn RD, Hermjakob H, Hubbard TJ, Jimenez RC, Jones P, Kähäri A, Kulesha E, Macías JR, Reeves GA, Prlic A. PMID: 18673527.
      View in: PubMed   Mentions: 51     Fields:    
    32. Integrating sequence and structural biology with DAS. BMC Bioinformatics. 2007 Sep 12; 8:333. Prlic A, Down TA, Kulesha E, Finn RD, Kähäri A, Hubbard TJ. PMID: 17850653.
      View in: PubMed   Mentions: 35     Fields:    
    33. New tools and expanded data analysis capabilities at the Protein Structure Prediction Center. Proteins. 2007; 69 Suppl 8:19-26. Kryshtafovych A, Prlic A, Dmytriv Z, Daniluk P, Milostan M, Eyrich V, Hubbard T, Fidelis K. PMID: 17705273.
      View in: PubMed   Mentions: 14     Fields:    Translation:Cells
    34. SISYPHUS--structural alignments for proteins with non-trivial relationships. Nucleic Acids Res. 2007 Jan; 35(Database issue):D253-9. Andreeva A, Prlic A, Hubbard TJ, Murzin AG. PMID: 17068077.
      View in: PubMed   Mentions: 27     Fields:    Translation:Cells
    35. Adding some SPICE to DAS. Bioinformatics. 2005 Sep 01; 21 Suppl 2:ii40-1. Prlic A, Down TA, Hubbard TJ. PMID: 16204122.
      View in: PubMed   Mentions: 29     Fields:    Translation:Cells
    36. WILMA-automated annotation of protein sequences. Bioinformatics. 2004 Jan 01; 20(1):127-8. Prlic A, Domingues FS, Lackner P, Sippl MJ. PMID: 14693821.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
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