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Items: 14


BioJava 5: A community driven open-source bioinformatics library.

Lafita A, Bliven S, Prlić A, Guzenko D, Rose PW, Bradley A, Pavan P, Myers-Turnbull D, Valasatava Y, Heuer M, Larson M, Burley SK, Duarte JM.

PLoS Comput Biol. 2019 Feb 8;15(2):e1006791. doi: 10.1371/journal.pcbi.1006791. [Epub ahead of print]


RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy.

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.

Nucleic Acids Res. 2019 Jan 8;47(D1):D464-D474. doi: 10.1093/nar/gky1004.


Protein Data Bank: the single global archive for 3D macromolecular structure data.

wwPDB consortium .

Nucleic Acids Res. 2019 Jan 8;47(D1):D520-D528. doi: 10.1093/nar/gky949.


NGL viewer: web-based molecular graphics for large complexes.

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

Bioinformatics. 2018 Nov 1;34(21):3755-3758. doi: 10.1093/bioinformatics/bty419.


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. Review.


To what extent do structural changes in catalytic metal sites affect enzyme function?

Valasatava Y, Rosato A, Furnham N, Thornton JM, Andreini C.

J Inorg Biochem. 2018 Feb;179:40-53. doi: 10.1016/j.jinorgbio.2017.11.002. Epub 2017 Nov 8.


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.


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.


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.


MetalPredator: a web server to predict iron-sulfur cluster binding proteomes.

Valasatava Y, Rosato A, Banci L, Andreini C.

Bioinformatics. 2016 Sep 15;32(18):2850-2. doi: 10.1093/bioinformatics/btw238. Epub 2016 Jun 6.


Minimal Functional Sites in Metalloproteins and Their Usage in Structural Bioinformatics.

Rosato A, Valasatava Y, Andreini C.

Int J Mol Sci. 2016 May 4;17(5). pii: E671. doi: 10.3390/ijms17050671. Review.


Hidden relationships between metalloproteins unveiled by structural comparison of their metal sites.

Valasatava Y, Andreini C, Rosato A.

Sci Rep. 2015 Mar 30;5:9486. doi: 10.1038/srep09486.


MetalS(3), a database-mining tool for the identification of structurally similar metal sites.

Valasatava Y, Rosato A, Cavallaro G, Andreini C.

J Biol Inorg Chem. 2014 Aug;19(6):937-45. doi: 10.1007/s00775-014-1128-3. Epub 2014 Apr 4.


MetalS2: a tool for the structural alignment of minimal functional sites in metal-binding proteins and nucleic acids.

Andreini C, Cavallaro G, Rosato A, Valasatava Y.

J Chem Inf Model. 2013 Nov 25;53(11):3064-75. doi: 10.1021/ci400459w. Epub 2013 Oct 28.


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