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Items: 1 to 50 of 236

1.

Investigation of protein quaternary structure via stoichiometry and symmetry ınformation.

Korkmaz S, Duarte JM, Prlić A, Goksuluk D, Zararsiz G, Saracbasi O, Burley SK, Rose PW.

PLoS One. 2018 Jun 4;13(6):e0197176. doi: 10.1371/journal.pone.0197176. eCollection 2018.

2.

Comparison of Alicyclobacillus acidocaldarius o-Succinylbenzoate Synthase to Its Promiscuous N-Succinylamino Acid Racemase/ o-Succinylbenzoate Synthase Relatives.

Odokonyero D, McMillan AW, Ramagopal UA, Toro R, Truong DP, Zhu M, Lopez MS, Somiari B, Herman M, Aziz A, Bonanno JB, Hull KG, Burley SK, Romo D, Almo SC, Glasner ME.

Biochemistry. 2018 Jul 3;57(26):3676-3689. doi: 10.1021/acs.biochem.8b00088. Epub 2018 May 30.

PMID:
29767960
3.

SOD1 Phosphorylation by mTORC1 Couples Nutrient Sensing and Redox Regulation.

Tsang CK, Chen M, Cheng X, Qi Y, Chen Y, Das I, Li X, Vallat B, Fu LW, Qian CN, Wang HY, White E, Burley SK, Zheng XFS.

Mol Cell. 2018 May 3;70(3):502-515.e8. doi: 10.1016/j.molcel.2018.03.029.

PMID:
29727620
4.

Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data.

Young JY, Westbrook JD, Feng Z, Peisach E, Persikova I, Sala R, Sen S, Berrisford JM, Swaminathan GJ, Oldfield TJ, Gutmanas A, Igarashi R, Armstrong DR, Baskaran K, Chen L, Chen M, Clark AR, Di Costanzo L, Dimitropoulos D, Gao G, Ghosh S, Gore S, Guranovic V, Hendrickx PMS, Hudson BP, Ikegawa Y, Kengaku Y, Lawson CL, Liang Y, Mak L, Mukhopadhyay A, Narayanan B, Nishiyama K, Patwardhan A, Sahni G, Sanz-García E, Sato J, Sekharan MR, Shao C, Smart OS, Tan L, van Ginkel G, Yang H, Zhuravleva MA, Markley JL, Nakamura H, Kurisu G, Kleywegt GJ, Velankar S, Berman HM, Burley SK.

Database (Oxford). 2018 Jan 1;2018. doi: 10.1093/database/bay002.

5.

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 Mar;36(3):272-281. doi: 10.1038/nbt.4072. Epub 2018 Feb 19.

PMID:
29457794
6.

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.

7.

D3R Grand Challenge 2: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies.

Gaieb Z, Liu S, Gathiaka S, Chiu M, Yang H, Shao C, Feher VA, Walters WP, Kuhn B, Rudolph MG, Burley SK, Gilson MK, Amaro RE.

J Comput Aided Mol Des. 2018 Jan;32(1):1-20. doi: 10.1007/s10822-017-0088-4. Epub 2017 Dec 4.

PMID:
29204945
8.

Validation of Structures in the Protein Data Bank.

Gore S, Sanz García E, Hendrickx PMS, Gutmanas A, Westbrook JD, Yang H, Feng Z, Baskaran K, Berrisford JM, Hudson BP, Ikegawa Y, Kobayashi N, Lawson CL, Mading S, Mak L, Mukhopadhyay A, Oldfield TJ, Patwardhan A, Peisach E, Sahni G, Sekharan MR, Sen S, Shao C, Smart OS, Ulrich EL, Yamashita R, Quesada M, Young JY, Nakamura H, Markley JL, Berman HM, Burley SK, Velankar S, Kleywegt GJ.

Structure. 2017 Dec 5;25(12):1916-1927. doi: 10.1016/j.str.2017.10.009. Epub 2017 Nov 22.

9.

RCSB Protein Data Bank: Sustaining a living digital data resource that enables breakthroughs in scientific research and biomedical education.

Burley SK, Berman HM, Christie C, Duarte JM, Feng Z, Westbrook J, Young J, Zardecki C.

Protein Sci. 2018 Jan;27(1):316-330. doi: 10.1002/pro.3331. Epub 2017 Nov 11. Review.

10.

PDB-Dev: a Prototype System for Depositing Integrative/Hybrid Structural Models.

Burley SK, Kurisu G, Markley JL, Nakamura H, Velankar S, Berman HM, Sali A, Schwede T, Trewhella J.

Structure. 2017 Sep 5;25(9):1317-1318. doi: 10.1016/j.str.2017.08.001.

11.

Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive.

Burley SK, Berman HM, Kleywegt GJ, Markley JL, Nakamura H, Velankar S.

Methods Mol Biol. 2017;1607:627-641. doi: 10.1007/978-1-4939-7000-1_26. Review.

12.

The hidden treasure in your data: phasing with unexpected weak anomalous scatterers from routine data sets.

Hegde RP, Fedorov AA, Sauder JM, Burley SK, Almo SC, Ramagopal UA.

Acta Crystallogr F Struct Biol Commun. 2017 Apr 1;73(Pt 4):184-195. doi: 10.1107/S2053230X17002680. Epub 2017 Mar 22.

PMID:
28368276
13.

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.

14.

Multivariate Analyses of Quality Metrics for Crystal Structures in the PDB Archive.

Shao C, Yang H, Westbrook JD, Young JY, Zardecki C, Burley SK.

Structure. 2017 Mar 7;25(3):458-468. doi: 10.1016/j.str.2017.01.013. Epub 2017 Feb 16.

15.

OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive.

Young JY, Westbrook JD, Feng Z, Sala R, Peisach E, Oldfield TJ, Sen S, Gutmanas A, Armstrong DR, Berrisford JM, Chen L, Chen M, Di Costanzo L, Dimitropoulos D, Gao G, Ghosh S, Gore S, Guranovic V, Hendrickx PMS, Hudson BP, Igarashi R, Ikegawa Y, Kobayashi N, Lawson CL, Liang Y, Mading S, Mak L, Mir MS, Mukhopadhyay A, Patwardhan A, Persikova I, Rinaldi L, Sanz-Garcia E, Sekharan MR, Shao C, Swaminathan GJ, Tan L, Ulrich EL, van Ginkel G, Yamashita R, Yang H, Zhuravleva MA, Quesada M, Kleywegt GJ, Berman HM, Markley JL, Nakamura H, Velankar S, Burley SK.

Structure. 2017 Mar 7;25(3):536-545. doi: 10.1016/j.str.2017.01.004. Epub 2017 Feb 9.

16.

A public database of macromolecular diffraction experiments.

Grabowski M, Langner KM, Cymborowski M, Porebski PJ, Sroka P, Zheng H, Cooper DR, Zimmerman MD, Elsliger MA, Burley SK, Minor W.

Acta Crystallogr D Struct Biol. 2016 Nov 1;72(Pt 11):1181-1193. Epub 2016 Oct 28.

17.

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.

18.

D3R grand challenge 2015: Evaluation of protein-ligand pose and affinity predictions.

Gathiaka S, Liu S, Chiu M, Yang H, Stuckey JA, Kang YN, Delproposto J, Kubish G, Dunbar JB Jr, Carlson HA, Burley SK, Walters WP, Amaro RE, Feher VA, Gilson MK.

J Comput Aided Mol Des. 2016 Sep;30(9):651-668. Epub 2016 Sep 30.

19.

Using the Tools and Resources of the RCSB Protein Data Bank.

Costanzo LD, Ghosh S, Zardecki C, Burley SK.

Curr Protoc Bioinformatics. 2016 Sep 7;55:1.9.1-1.9.35. doi: 10.1002/cpbi.13.

PMID:
27603019
20.

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.

21.

The archiving and dissemination of biological structure data.

Berman HM, Burley SK, Kleywegt GJ, Markley JL, Nakamura H, Velankar S.

Curr Opin Struct Biol. 2016 Oct;40:17-22. doi: 10.1016/j.sbi.2016.06.018. Epub 2016 Jul 21. Review.

22.

DCC: a Swiss army knife for structure factor analysis and validation.

Yang H, Peisach E, Westbrook JD, Young J, Berman HM, Burley SK.

J Appl Crystallogr. 2016 Apr 18;49(Pt 3):1081-1084. eCollection 2016 Jun 1.

23.

Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop.

Adams PD, Aertgeerts K, Bauer C, Bell JA, Berman HM, Bhat TN, Blaney JM, Bolton E, Bricogne G, Brown D, Burley SK, Case DA, Clark KL, Darden T, Emsley P, Feher VA, Feng Z, Groom CR, Harris SF, Hendle J, Holder T, Joachimiak A, Kleywegt GJ, Krojer T, Marcotrigiano J, Mark AE, Markley JL, Miller M, Minor W, Montelione GT, Murshudov G, Nakagawa A, Nakamura H, Nicholls A, Nicklaus M, Nolte RT, Padyana AK, Peishoff CE, Pieniazek S, Read RJ, Shao C, Sheriff S, Smart O, Soisson S, Spurlino J, Stouch T, Svobodova R, Tempel W, Terwilliger TC, Tronrud D, Velankar S, Ward SC, Warren GL, Westbrook JD, Williams P, Yang H, Young J.

Structure. 2016 Apr 5;24(4):502-508. doi: 10.1016/j.str.2016.02.017.

24.

Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop.

Sali A, Berman HM, Schwede T, Trewhella J, Kleywegt G, Burley SK, Markley J, Nakamura H, Adams P, Bonvin AM, Chiu W, Peraro MD, Di Maio F, Ferrin TE, Grünewald K, Gutmanas A, Henderson R, Hummer G, Iwasaki K, Johnson G, Lawson CL, Meiler J, Marti-Renom MA, Montelione GT, Nilges M, Nussinov R, Patwardhan A, Rappsilber J, Read RJ, Saibil H, Schröder GF, Schwieters CD, Seidel CA, Svergun D, Topf M, Ulrich EL, Velankar S, Westbrook JD.

Structure. 2015 Jul 7;23(7):1156-67. doi: 10.1016/j.str.2015.05.013. Epub 2015 Jun 18.

25.

The RCSB PDB "Molecule of the Month": Inspiring a Molecular View of Biology.

Goodsell DS, Dutta S, Zardecki C, Voigt M, Berman HM, Burley SK.

PLoS Biol. 2015 May 5;13(5):e1002140. doi: 10.1371/journal.pbio.1002140. eCollection 2015 May.

26.

Identification of a Non-Gatekeeper Hot Spot for Drug-Resistant Mutations in mTOR Kinase.

Wu TJ, Wang X, Zhang Y, Meng L, Kerrigan JE, Burley SK, Zheng XF.

Cell Rep. 2015 Apr 21;11(3):446-59. doi: 10.1016/j.celrep.2015.03.040. Epub 2015 Apr 9.

27.

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.

28.

Response to On prompt update of literature references in the Protein Data Bank.

Berman HM, Burley SK, Kleywegt GJ, Nakamura H, Markley JL.

Acta Crystallogr D Biol Crystallogr. 2014 Oct;70(Pt 10):2780. doi: 10.1107/S1399004714020513. Epub 2014 Sep 30.

29.

Crystal structure of Clostridium acetobutylicum Aspartate kinase (CaAK): An important allosteric enzyme for amino acids production.

Manjasetty BA, Chance MR, Burley SK, Panjikar S, Almo SC.

Biotechnol Rep (Amst). 2014 Sep 1;3:73-85.

30.

Integrative structure-function mapping of the nucleoporin Nup133 suggests a conserved mechanism for membrane anchoring of the nuclear pore complex.

Kim SJ, Fernandez-Martinez J, Sampathkumar P, Martel A, Matsui T, Tsuruta H, Weiss TM, Shi Y, Markina-Inarrairaegui A, Bonanno JB, Sauder JM, Burley SK, Chait BT, Almo SC, Rout MP, Sali A.

Mol Cell Proteomics. 2014 Nov;13(11):2911-26. doi: 10.1074/mcp.M114.040915. Epub 2014 Aug 19.

31.

Functional annotation and structural characterization of a novel lactonase hydrolyzing D-xylono-1,4-lactone-5-phosphate and L-arabino-1,4-lactone-5-phosphate.

Korczynska M, Xiang DF, Zhang Z, Xu C, Narindoshvili T, Kamat SS, Williams HJ, Chang SS, Kolb P, Hillerich B, Sauder JM, Burley SK, Almo SC, Swaminathan S, Shoichet BK, Raushel FM.

Biochemistry. 2014 Jul 22;53(28):4727-38. doi: 10.1021/bi500595c. Epub 2014 Jul 9.

32.

Loss of quaternary structure is associated with rapid sequence divergence in the OSBS family.

Odokonyero D, Sakai A, Patskovsky Y, Malashkevich VN, Fedorov AA, Bonanno JB, Fedorov EV, Toro R, Agarwal R, Wang C, Ozerova ND, Yew WS, Sauder JM, Swaminathan S, Burley SK, Almo SC, Glasner ME.

Proc Natl Acad Sci U S A. 2014 Jun 10;111(23):8535-40. doi: 10.1073/pnas.1318703111. Epub 2014 May 28.

33.

Divergent evolution of ligand binding in the o-succinylbenzoate synthase family.

Odokonyero D, Ragumani S, Lopez MS, Bonanno JB, Ozerova ND, Woodard DR, Machala BW, Swaminathan S, Burley SK, Almo SC, Glasner ME.

Biochemistry. 2013 Oct 22;52(42):7512-21. doi: 10.1021/bi401176d. Epub 2013 Oct 9.

34.

Structural basis for the divergence of substrate specificity and biological function within HAD phosphatases in lipopolysaccharide and sialic acid biosynthesis.

Daughtry KD, Huang H, Malashkevich V, Patskovsky Y, Liu W, Ramagopal U, Sauder JM, Burley SK, Almo SC, Dunaway-Mariano D, Allen KN.

Biochemistry. 2013 Aug 13;52(32):5372-86. doi: 10.1021/bi400659k. Epub 2013 Jul 29.

35.

Revealing structural views of biology.

Goodsell DS, Burley SK, Berman HM.

Biopolymers. 2013 Nov;99(11):817-24. doi: 10.1002/bip.22338.

36.

Protein production from the structural genomics perspective: achievements and future needs.

Almo SC, Garforth SJ, Hillerich BS, Love JD, Seidel RD, Burley SK.

Curr Opin Struct Biol. 2013 Jun;23(3):335-44. doi: 10.1016/j.sbi.2013.02.014. Epub 2013 May 1. Review.

37.

Structure, dynamics, evolution, and function of a major scaffold component in the nuclear pore complex.

Sampathkumar P, Kim SJ, Upla P, Rice WJ, Phillips J, Timney BL, Pieper U, Bonanno JB, Fernandez-Martinez J, Hakhverdyan Z, Ketaren NE, Matsui T, Weiss TM, Stokes DL, Sauder JM, Burley SK, Sali A, Rout MP, Almo SC.

Structure. 2013 Apr 2;21(4):560-71. doi: 10.1016/j.str.2013.02.005. Epub 2013 Mar 14.

38.

Structure of alanine racemase from Oenococcus oeni with bound pyridoxal 5'-phosphate.

Palani K, Burley SK, Swaminathan S.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2013 Jan 1;69(Pt 1):15-9. doi: 10.1107/S1744309112047276. Epub 2012 Dec 25.

39.

PDB40: The Protein Data Bank celebrates its 40th birthday.

Burley SK.

Biopolymers. 2013 Mar;99(3):165-7. doi: 10.1002/bip.22182. No abstract available.

PMID:
23280389
40.

Structure of a periplasmic glucose-binding protein from Thermotoga maritima.

Palani K, Kumaran D, Burley SK, Swaminathan S.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2012 Dec 1;68(Pt 12):1460-4. doi: 10.1107/S1744309112045241. Epub 2012 Nov 19.

41.

1-methylthio-D-xylulose 5-phosphate methylsulfurylase: a novel route to 1-deoxy-D-xylulose 5-phosphate in Rhodospirillum rubrum.

Warlick BP, Evans BS, Erb TJ, Ramagopal UA, Sriram J, Imker HJ, Sauder JM, Bonanno JB, Burley SK, Tabita FR, Almo SC, Sweedler JS, Gerlt JA.

Biochemistry. 2012 Oct 23;51(42):8324-6. doi: 10.1021/bi301215g. Epub 2012 Oct 8.

42.

Cas5d processes pre-crRNA and is a member of a larger family of CRISPR RNA endonucleases.

Garside EL, Schellenberg MJ, Gesner EM, Bonanno JB, Sauder JM, Burley SK, Almo SC, Mehta G, MacMillan AM.

RNA. 2012 Nov;18(11):2020-8. doi: 10.1261/rna.033100.112. Epub 2012 Sep 24.

43.

Atomic structure of the nuclear pore complex targeting domain of a Nup116 homologue from the yeast, Candida glabrata.

Sampathkumar P, Kim SJ, Manglicmot D, Bain KT, Gilmore J, Gheyi T, Phillips J, Pieper U, Fernandez-Martinez J, Franke JD, Matsui T, Tsuruta H, Atwell S, Thompson DA, Emtage JS, Wasserman SR, Rout MP, Sali A, Sauder JM, Almo SC, Burley SK.

Proteins. 2012 Aug;80(8):2110-6. doi: 10.1002/prot.24102. Epub 2012 Jun 4.

44.

Rapid-access, high-throughput synchrotron crystallography for drug discovery.

Wasserman SR, Koss JW, Sojitra ST, Morisco LL, Burley SK.

Trends Pharmacol Sci. 2012 May;33(5):261-7. doi: 10.1016/j.tips.2012.03.009. Epub 2012 Apr 18. Review.

PMID:
22521107
45.

Structure and catalytic mechanism of LigI: insight into the amidohydrolase enzymes of cog3618 and lignin degradation.

Hobbs ME, Malashkevich V, Williams HJ, Xu C, Sauder JM, Burley SK, Almo SC, Raushel FM.

Biochemistry. 2012 Apr 24;51(16):3497-507. doi: 10.1021/bi300307b. Epub 2012 Apr 9.

46.

Structural insight into mechanism and diverse substrate selection strategy of L-ribulokinase.

Agarwal R, Burley SK, Swaminathan S.

Proteins. 2012 Jan;80(1):261-8. doi: 10.1002/prot.23202. Epub 2011 Nov 9.

47.

The catalase activity of diiron adenine deaminase.

Kamat SS, Holmes-Hampton GP, Bagaria A, Kumaran D, Tichy SE, Gheyi T, Zheng X, Bain K, Groshong C, Emtage S, Sauder JM, Burley SK, Swaminathan S, Lindahl PA, Raushel FM.

Protein Sci. 2011 Dec;20(12):2080-94. doi: 10.1002/pro.748. Epub 2011 Nov 9.

48.

Structural variation in bacterial glyoxalase I enzymes: investigation of the metalloenzyme glyoxalase I from Clostridium acetobutylicum.

Suttisansanee U, Lau K, Lagishetty S, Rao KN, Swaminathan S, Sauder JM, Burley SK, Honek JF.

J Biol Chem. 2011 Nov 4;286(44):38367-74. doi: 10.1074/jbc.M111.251603. Epub 2011 Sep 13.

49.

Gimme phospho-serine five! Capping enzyme guanylyltransferase recognition of the RNA polymerase II CTD.

Burley SK, Sonenberg N.

Mol Cell. 2011 Jul 22;43(2):163-5. doi: 10.1016/j.molcel.2011.07.003.

50.

Protein-RNA and protein-protein recognition by dual KH1/2 domains of the neuronal splicing factor Nova-1.

Teplova M, Malinina L, Darnell JC, Song J, Lu M, Abagyan R, Musunuru K, Teplov A, Burley SK, Darnell RB, Patel DJ.

Structure. 2011 Jul 13;19(7):930-44. doi: 10.1016/j.str.2011.05.002.

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