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Items: 43

1.

Recon3D enables a three-dimensional view of gene variation in human metabolism.

Brunk E, Sahoo S, Zielinski DC, Altunkaya A, Dräger A, Mih N, Gatto F, Nilsson A, Preciat Gonzalez GA, Aurich MK, Prlić A, Sastry A, Danielsdottir AD, Heinken A, Noronha A, Rose PW, Burley SK, Fleming RMT, Nielsen J, Thiele I, Palsson BO.

Nat Biotechnol. 2018 Feb 19. doi: 10.1038/nbt.4072. [Epub ahead of print]

PMID:
29457794
2.

Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework.

Glusman G, Rose PW, Prlić 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.

Genome Med. 2017 Dec 18;9(1):113. doi: 10.1186/s13073-017-0509-y.

3.

MMTF-An efficient file format for the transmission, visualization, and analysis of macromolecular structures.

Bradley AR, Rose AS, Pavelka A, Valasatava Y, Duarte JM, Prlić A, Rose PW.

PLoS Comput Biol. 2017 Jun 2;13(6):e1005575. doi: 10.1371/journal.pcbi.1005575. eCollection 2017 Jun.

4.

Towards an efficient compression of 3D coordinates of macromolecular structures.

Valasatava Y, Bradley AR, Rose AS, Duarte JM, Prlić A, Rose PW.

PLoS One. 2017 Mar 31;12(3):e0174846. doi: 10.1371/journal.pone.0174846. eCollection 2017.

5.

BioJava-ModFinder: identification of protein modifications in 3D structures from the Protein Data Bank.

Gao J, Prlic A, Bi C, Bluhm WF, Dimitropoulos D, Xu D, Bourne PE, Rose PW.

Bioinformatics. 2017 Jul 1;33(13):2047-2049. doi: 10.1093/bioinformatics/btx101.

PMID:
28334105
6.

Impact of genetic variation on three dimensional structure and function of proteins.

Bhattacharya R, Rose PW, Burley SK, Prlić A.

PLoS One. 2017 Mar 15;12(3):e0171355. doi: 10.1371/journal.pone.0171355. eCollection 2017.

7.

The RCSB protein data bank: integrative view of protein, gene and 3D structural information.

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.

Nucleic Acids Res. 2017 Jan 4;45(D1):D271-D281. doi: 10.1093/nar/gkw1000. Epub 2016 Oct 27.

8.

Integrating genomic information with protein sequence and 3D atomic level structure at the RCSB protein data bank.

Prlic A, Kalro T, Bhattacharya R, Christie C, Burley SK, Rose PW.

Bioinformatics. 2016 Dec 15;32(24):3833-3835. doi: 10.1093/bioinformatics/btw547. Epub 2016 Aug 22.

9.

Detection of circular permutations within protein structures using CE-CP.

Bliven SE, Bourne PE, Prlić A.

Bioinformatics. 2015 Apr 15;31(8):1316-8. doi: 10.1093/bioinformatics/btu823. Epub 2014 Dec 12.

10.

The RCSB Protein Data Bank: views of structural biology for basic and applied research and education.

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.

Nucleic Acids Res. 2015 Jan;43(Database issue):D345-56. doi: 10.1093/nar/gku1214. Epub 2014 Nov 26.

11.

RCSB PDB Mobile: iOS and Android mobile apps to provide data access and visualization to the RCSB Protein Data Bank.

Quinn GB, Bi C, Christie CH, Pang K, Prlić A, Nakane T, Zardecki C, Voigt M, Berman HM, Bourne PE, Rose PW.

Bioinformatics. 2015 Jan 1;31(1):126-7. doi: 10.1093/bioinformatics/btu596. Epub 2014 Sep 2.

12.

Systematic detection of internal symmetry in proteins using CE-Symm.

Myers-Turnbull D, Bliven SE, Rose PW, Aziz ZK, Youkharibache P, Bourne PE, Prlić A.

J Mol Biol. 2014 May 29;426(11):2255-68. doi: 10.1016/j.jmb.2014.03.010. Epub 2014 Mar 26.

13.

Trendspotting in the Protein Data Bank.

Berman HM, Coimbatore Narayanan B, Di Costanzo L, Dutta S, Ghosh S, Hudson BP, Lawson CL, Peisach E, Prlić A, Rose PW, Shao C, Yang H, Young J, Zardecki C.

FEBS Lett. 2013 Apr 17;587(8):1036-45. doi: 10.1016/j.febslet.2012.12.029. Epub 2013 Jan 18. Review.

14.

Ten simple rules for the open development of scientific software.

Prlić A, Procter JB.

PLoS Comput Biol. 2012;8(12):e1002802. doi: 10.1371/journal.pcbi.1002802. Epub 2012 Dec 6. No abstract available.

15.

The RCSB Protein Data Bank: new resources for research and education.

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.

Nucleic Acids Res. 2013 Jan;41(Database issue):D475-82. doi: 10.1093/nar/gks1200. Epub 2012 Nov 27.

16.

BioJava: an open-source framework for bioinformatics in 2012.

Prlić 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.

Bioinformatics. 2012 Oct 15;28(20):2693-5. doi: 10.1093/bioinformatics/bts494. Epub 2012 Aug 9.

17.

Circular permutation in proteins.

Bliven S, Prlić A.

PLoS Comput Biol. 2012;8(3):e1002445. doi: 10.1371/journal.pcbi.1002445. Epub 2012 Mar 29. No abstract available.

18.

The importance of thorough preoperative diagnostics of maxillary ameloblastoma: report of three cases.

Matijević M, Leović D, Popić B, Zubcić V, Kopić V, Prlić A, Siber S, Dinjar K.

Coll Antropol. 2010 Dec;34(4):1445-8.

PMID:
21874736
19.

Quality of life of patients after stroke in county Osijek-Baranya.

Prlić N, Kadojić D, Kadojić M, Gmajnić R, Prlić A.

Coll Antropol. 2010 Dec;34(4):1379-90.

PMID:
21874725
20.

Quality assurance for the query and distribution systems of the RCSB Protein Data Bank.

Bluhm WF, Beran B, Bi C, Dimitropoulos D, Prlic A, Quinn GB, Rose PW, Shah C, Young J, Yukich B, Berman HM, Bourne PE.

Database (Oxford). 2011 Mar 7;2011:bar003. doi: 10.1093/database/bar003. Print 2011.

21.

The RCSB Protein Data Bank: redesigned web site and web services.

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.

Nucleic Acids Res. 2011 Jan;39(Database issue):D392-401. doi: 10.1093/nar/gkq1021. Epub 2010 Oct 29.

22.

Pre-calculated protein structure alignments at the RCSB PDB website.

Prlic A, Bliven S, Rose PW, Bluhm WF, Bizon C, Godzik A, Bourne PE.

Bioinformatics. 2010 Dec 1;26(23):2983-5. doi: 10.1093/bioinformatics/btq572. Epub 2010 Oct 10.

23.

Integration of open access literature into the RCSB Protein Data Bank using BioLit.

Prlić A, Martinez MA, Dimitropoulos D, Beran B, Yukich BT, Rose PW, Bourne PE, Fink JL.

BMC Bioinformatics. 2010 Apr 29;11:220. doi: 10.1186/1471-2105-11-220.

24.

Will widgets and semantic tagging change computational biology?

Bourne PE, Beran B, Bi C, Bluhm W, Dunbrack R, Prlić A, Quinn G, Rose P, Shah R, Tao W, Weitzner B, Yukich B.

PLoS Comput Biol. 2010 Feb 26;6(2):e1000673. doi: 10.1371/journal.pcbi.1000673. No abstract available.

25.

Regional pattern of smoking in Croatia.

Samardzić S, Marvinac GV, Prlić A.

Coll Antropol. 2009 Apr;33 Suppl 1:43-6.

PMID:
19563146
26.

Proportions in the upper lip-lower lip-chin area of the lower face as determined by photogrammetric method.

Anic-Milosevic S, Mestrovic S, Prlić A, Slaj M.

J Craniomaxillofac Surg. 2010 Mar;38(2):90-5. doi: 10.1016/j.jcms.2009.03.013. Epub 2009 May 17.

PMID:
19447641
27.

DASMI: exchanging, annotating and assessing molecular interaction data.

Blankenburg H, Finn RD, Prlić A, Jenkinson AM, Ramírez F, Emig D, Schelhorn SE, Büch J, Lengauer T, Albrecht M.

Bioinformatics. 2009 May 15;25(10):1321-8. doi: 10.1093/bioinformatics/btp142.

28.

The Protein Feature Ontology: a tool for the unification of protein feature annotations.

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.

Bioinformatics. 2008 Dec 1;24(23):2767-72. doi: 10.1093/bioinformatics/btn528. Epub 2008 Oct 20.

29.

BioJava: an open-source framework for bioinformatics.

Holland RC, Down TA, Pocock M, Prlić A, Huen D, James K, Foisy S, Dräger A, Yates A, Heuer M, Schreiber MJ.

Bioinformatics. 2008 Sep 15;24(18):2096-7. doi: 10.1093/bioinformatics/btn397. Epub 2008 Aug 8.

30.

Integrating biological data--the Distributed Annotation System.

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, Prlić A.

BMC Bioinformatics. 2008 Jul 22;9 Suppl 8:S3. doi: 10.1186/1471-2105-9-S8-S3.

31.

Ensembl 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, Gräf S, Haider S, Hammond M, Holland R, Howe KL, Howe K, Johnson N, Jenkinson A, Kähäri 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.

Nucleic Acids Res. 2008 Jan;36(Database issue):D707-14. Epub 2007 Nov 13.

32.

Integrating sequence and structural biology with DAS.

Prlić A, Down TA, Kulesha E, Finn RD, Kähäri A, Hubbard TJ.

BMC Bioinformatics. 2007 Sep 12;8:333.

33.

New tools and expanded data analysis capabilities at the Protein Structure Prediction Center.

Kryshtafovych A, Prlic A, Dmytriv Z, Daniluk P, Milostan M, Eyrich V, Hubbard T, Fidelis K.

Proteins. 2007;69 Suppl 8:19-26.

34.

Ensembl 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.

Nucleic Acids Res. 2007 Jan;35(Database issue):D610-7. Epub 2006 Dec 5.

35.

SISYPHUS--structural alignments for proteins with non-trivial relationships.

Andreeva A, Prlić A, Hubbard TJ, Murzin AG.

Nucleic Acids Res. 2007 Jan;35(Database issue):D253-9. Epub 2006 Oct 26.

36.

Ensembl 2006.

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, Gräf S, Hammond M, Herrero J, Howe K, Iyer V, Jekosch K, Kähäri 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.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D556-61.

37.

Adding some SPICE to DAS.

Prlić A, Down TA, Hubbard TJ.

Bioinformatics. 2005 Sep 1;21 Suppl 2:ii40-1.

38.

WILMA-automated annotation of protein sequences.

Prlić A, Domingues FS, Lackner P, Sippl MJ.

Bioinformatics. 2004 Jan 1;20(1):127-8.

PMID:
14693821
39.

Assessment of the CASP4 fold recognition category.

Sippl MJ, Lackner P, Domingues FS, Prlić A, Malik R, Andreeva A, Wiederstein M.

Proteins. 2001;Suppl 5:55-67.

PMID:
11835482
40.

Structure-derived substitution matrices for alignment of distantly related sequences.

Prlić A, Domingues FS, Sippl MJ.

Protein Eng. 2000 Aug;13(8):545-50.

PMID:
10964983
41.

Sustained performance of knowledge-based potentials in fold recognition.

Domingues FS, Koppensteiner WA, Jaritz M, Prlic A, Weichenberger C, Wiederstein M, Floeckner H, Lackner P, Sippl MJ.

Proteins. 1999;Suppl 3:112-20.

PMID:
10526359
42.

Partial laryngectomy in transglottic carcinoma.

Prlić A, Krajina Z.

Acta Med Croatica. 1992;46(1):37-9.

PMID:
1380357
43.

[Corrosion of the esophagus treated at the ENT department of the Osijek general hospital between 1967 and 1976 (author's transl)].

Prlić A, Spralja V, Dimter E.

Lijec Vjesn. 1979 Jan;101(1):43-4. Croatian. No abstract available.

PMID:
449582

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