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Items: 1 to 50 of 267

1.

RCSB Protein Data Bank: Enabling biomedical research and drug discovery.

Goodsell DS, Zardecki C, Di Costanzo L, Duarte JM, Hudson BP, Persikova I, Segura J, Shao C, Voigt M, Westbrook JD, Young JY, Burley SK.

Protein Sci. 2019 Sep 18. doi: 10.1002/pro.3730. [Epub ahead of print]

PMID:
31531901
2.

Continuous Evaluation of Ligand Protein Predictions: A Weekly Community Challenge for Drug Docking.

Wagner JR, Churas CP, Liu S, Swift RV, Chiu M, Shao C, Feher VA, Burley SK, Gilson MK, Amaro RE.

Structure. 2019 Aug 6;27(8):1326-1335.e4. doi: 10.1016/j.str.2019.05.012. Epub 2019 Jun 27.

PMID:
31257108
3.

A Novel Acquired Exon 20 EGFR M766Q Mutation in Lung Adenocarcinoma Mediates Osimertinib Resistance but is Sensitive to Neratinib and Poziotinib.

Castellano GM, Aisner J, Burley SK, Vallat B, Yu HA, Pine SR, Ganesan S.

J Thorac Oncol. 2019 Jun 27. pii: S1556-0864(19)30495-2. doi: 10.1016/j.jtho.2019.06.015. [Epub ahead of print]

PMID:
31254668
4.

The Effects of Sleep Loss on Military Physical Performance.

Grandou C, Wallace L, Fullagar HHK, Duffield R, Burley S.

Sports Med. 2019 Aug;49(8):1159-1172. doi: 10.1007/s40279-019-01123-8. Review.

PMID:
31102110
5.

Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the Protein Data Bank (PDB).

Adams PD, Afonine PV, Baskaran K, Berman HM, Berrisford J, Bricogne G, Brown DG, Burley SK, Chen M, Feng Z, Flensburg C, Gutmanas A, Hoch JC, Ikegawa Y, Kengaku Y, Krissinel E, Kurisu G, Liang Y, Liebschner D, Mak L, Markley JL, Moriarty NW, Murshudov GN, Noble M, Peisach E, Persikova I, Poon BK, Sobolev OV, Ulrich EL, Velankar S, Vonrhein C, Westbrook J, Wojdyr M, Yokochi M, Young JY.

Acta Crystallogr D Struct Biol. 2019 Apr 1;75(Pt 4):451-454. doi: 10.1107/S2059798319004522. Epub 2019 Apr 8. No abstract available.

PMID:
30988261
6.

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. eCollection 2019 Feb.

7.

D3R Grand Challenge 3: blind prediction of protein-ligand poses and affinity rankings.

Gaieb Z, Parks CD, Chiu M, Yang H, Shao C, Walters WP, Lambert MH, Nevins N, Bembenek SD, Ameriks MK, Mirzadegan T, Burley SK, Amaro RE, Gilson MK.

J Comput Aided Mol Des. 2019 Jan;33(1):1-18. doi: 10.1007/s10822-018-0180-4. Epub 2019 Jan 10.

PMID:
30632055
8.

Integrative/Hybrid Methods Structural Biology: Role of Macromolecular Crystallography.

Burley SK.

Adv Exp Med Biol. 2018;1105:11-18. doi: 10.1007/978-981-13-2200-6_2. Review.

PMID:
30617820
9.

How Structural Biologists and the Protein Data Bank Contributed to Recent FDA New Drug Approvals.

Westbrook JD, Burley SK.

Structure. 2019 Feb 5;27(2):211-217. doi: 10.1016/j.str.2018.11.007. Epub 2018 Dec 27. Review.

10.

Outlier analyses of the Protein Data Bank archive using a probability-density-ranking approach.

Shao C, Liu Z, Yang H, Wang S, Burley SK.

Sci Data. 2018 Dec 11;5:180293. doi: 10.1038/sdata.2018.293.

11.

Amino acid modifications for conformationally constraining naturally occurring and engineered peptide backbones: Insights from the Protein Data Bank.

Di Costanzo L, Dutta S, Burley SK.

Biopolymers. 2018 Aug;109(10):e23230. doi: 10.1002/bip.23230. Epub 2018 Oct 25. Review.

PMID:
30368772
12.

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.

13.

Analysis of impact metrics for the Protein Data Bank.

Markosian C, Di Costanzo L, Sekharan M, Shao C, Burley SK, Zardecki C.

Sci Data. 2018 Oct 16;5:180212. doi: 10.1038/sdata.2018.212.

14.

Primary Contact Occupational Therapy Hand Clinics: The pull of an occupational perspective.

Burley S, Cox R, Di Tommaso A, Molineux M.

Aust Occup Ther J. 2018 Dec;65(6):533-543. doi: 10.1111/1440-1630.12507. Epub 2018 Aug 22.

PMID:
30132914
15.

Positive, limited and negative responders: The variability in physical fitness adaptation to basic military training.

Burley SD, Drain JR, Sampson JA, Groeller H.

J Sci Med Sport. 2018 Nov;21(11):1168-1172. doi: 10.1016/j.jsams.2018.06.018. Epub 2018 Jul 7.

16.

Investigation of protein quaternary structure via stoichiometry and symmetry information.

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. Erratum in: PLoS One. 2018 Jul 27;13(7):e0201403.

17.

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
18.

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.

19.

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.

20.

The LiveWell Dorset behaviour change system.

Crowe S, Burley S, Long S.

Perspect Public Health. 2018 Mar;138(2):83-84. doi: 10.1177/1757913917751795. No abstract available.

PMID:
29465013
21.

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.

22.

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.

23.

Longitudinal deformation bench testing using a coronary artery model: a new standard?

Choudhury TR, Al-Saigh S, Burley S, Li L, Shakhshir N, Mirhosseini N, Wang T, Arnous S, Khan MA, Mamas MA, Fraser DGW.

Open Heart. 2017 Nov 6;4(2):e000537. doi: 10.1136/openhrt-2016-000537. eCollection 2017.

24.

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.

25.

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.

26.

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.

27.

Hormonal response patterns are differentially influenced by physical conditioning programs during basic military training.

Drain JR, Groeller H, Burley SD, Nindl BC.

J Sci Med Sport. 2017 Nov;20 Suppl 4:S98-S103. doi: 10.1016/j.jsams.2017.08.020. Epub 2017 Sep 6.

PMID:
28927970
28.

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.

29.

Can promoting awareness of fetal movements and focusing interventions reduce fetal mortality? A stepped-wedge cluster randomised trial (AFFIRM).

Heazell AEP, Weir CJ, Stock SJE, Calderwood CJ, Burley SC, Froen JF, Geary M, Hunter A, McAuliffe FM, Murdoch E, Rodriguez A, Ross-Davie M, Scott J, Whyte S, Norman JE.

BMJ Open. 2017 Aug 11;7(8):e014813. doi: 10.1136/bmjopen-2016-014813.

30.

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.

31.

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.

32.

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.

33.

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.

34.

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.

35.

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.

36.

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.

37.

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.

38.

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
39.

The Differential Hormonal Milieu of Morning versus Evening May Have an Impact on Muscle Hypertrophic Potential.

Burley SD, Whittingham-Dowd J, Allen J, Grosset JF, Onambele-Pearson GL.

PLoS One. 2016 Sep 1;11(9):e0161500. doi: 10.1371/journal.pone.0161500. eCollection 2016.

40.

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.

41.

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.

42.

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.

43.

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.

44.

The Effectiveness of Basic Military Training To Improve Functional Lifting Strength in New Recruits.

Drain JR, Sampson JA, Billing DC, Burley SD, Linnane DM, Groeller H.

J Strength Cond Res. 2015 Nov;29 Suppl 11:S173-7. doi: 10.1519/JSC.0000000000001072.

PMID:
26506184
45.

How Effective Is Initial Military-Specific Training in the Development of Physical Performance of Soldiers?

Groeller H, Burley S, Orchard P, Sampson JA, Billing DC, Linnane D.

J Strength Cond Res. 2015 Nov;29 Suppl 11:S158-62. doi: 10.1519/JSC.0000000000001066.

PMID:
26506181
46.

Employment Standards for Australian Urban Firefighters: Part 2: The Physiological Demands and the Criterion Tasks.

Taylor NA, Fullagar HH, Sampson JA, Notley SR, Burley SD, Lee DS, Groeller H.

J Occup Environ Med. 2015 Oct;57(10):1072-82. doi: 10.1097/JOM.0000000000000526. Erratum in: J Occup Environ Med. 2015 Dec;57(12):e159.

PMID:
26461862
47.

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.

48.

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.

49.

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.

50.

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.

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