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Items: 1 to 20 of 45

1.

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation.

Hess B, Kutzner C, van der Spoel D, Lindahl E.

J Chem Theory Comput. 2008 Mar;4(3):435-47. doi: 10.1021/ct700301q.

PMID:
26620784
2.

OpenMM: A Hardware Independent Framework for Molecular Simulations.

Eastman P, Pande VS.

Comput Sci Eng. 2015 Jul 1;12(4):34-39.

3.

Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach.

Lasker K, Förster F, Bohn S, Walzthoeni T, Villa E, Unverdorben P, Beck F, Aebersold R, Sali A, Baumeister W.

Proc Natl Acad Sci U S A. 2012 Jan 31;109(5):1380-7. doi: 10.1073/pnas.1120559109. Epub 2012 Jan 23.

4.

UCSF Chimera, MODELLER, and IMP: an integrated modeling system.

Yang Z, Lasker K, Schneidman-Duhovny D, Webb B, Huang CC, Pettersen EF, Goddard TD, Meng EC, Sali A, Ferrin TE.

J Struct Biol. 2012 Sep;179(3):269-78. doi: 10.1016/j.jsb.2011.09.006. Epub 2011 Sep 22.

5.

ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules.

Leaver-Fay A, Tyka M, Lewis SM, Lange OF, Thompson J, Jacak R, Kaufman K, Renfrew PD, Smith CA, Sheffler W, Davis IW, Cooper S, Treuille A, Mandell DJ, Richter F, Ban YE, Fleishman SJ, Corn JE, Kim DE, Lyskov S, Berrondo M, Mentzer S, Popović Z, Havranek JJ, Karanicolas J, Das R, Meiler J, Kortemme T, Gray JJ, Kuhlman B, Baker D, Bradley P.

Methods Enzymol. 2011;487:545-74. doi: 10.1016/B978-0-12-381270-4.00019-6.

6.

The three-dimensional folding of the α-globin gene domain reveals formation of chromatin globules.

Baù D, Sanyal A, Lajoie BR, Capriotti E, Byron M, Lawrence JB, Dekker J, Marti-Renom MA.

Nat Struct Mol Biol. 2011 Jan;18(1):107-14. doi: 10.1038/nsmb.1936. Epub 2010 Dec 5.

7.

ModBase, a database of annotated comparative protein structure models, and associated resources.

Pieper U, Webb BM, Barkan DT, Schneidman-Duhovny D, Schlessinger A, Braberg H, Yang Z, Meng EC, Pettersen EF, Huang CC, Datta RS, Sampathkumar P, Madhusudhan MS, Sjölander K, Ferrin TE, Burley SK, Sali A.

Nucleic Acids Res. 2011 Jan;39(Database issue):D465-74. doi: 10.1093/nar/gkq1091. Epub 2010 Nov 19.

8.

The BioGRID Interaction Database: 2011 update.

Stark C, Breitkreutz BJ, Chatr-Aryamontri A, Boucher L, Oughtred R, Livstone MS, Nixon J, Van Auken K, Wang X, Shi X, Reguly T, Rust JM, Winter A, Dolinski K, Tyers M.

Nucleic Acids Res. 2011 Jan;39(Database issue):D698-704. doi: 10.1093/nar/gkq1116. Epub 2010 Nov 11.

9.

Computational science: ...Error.

Merali Z.

Nature. 2010 Oct 14;467(7317):775-7. doi: 10.1038/467775a. No abstract available.

PMID:
20944712
10.

Publish your computer code: it is good enough.

Barnes N.

Nature. 2010 Oct 14;467(7317):753. doi: 10.1038/467753a. No abstract available.

PMID:
20944687
11.

EMDataBank.org: unified data resource for CryoEM.

Lawson CL, Baker ML, Best C, Bi C, Dougherty M, Feng P, van Ginkel G, Devkota B, Lagerstedt I, Ludtke SJ, Newman RH, Oldfield TJ, Rees I, Sahni G, Sala R, Velankar S, Warren J, Westbrook JD, Henrick K, Kleywegt GJ, Berman HM, Chiu W.

Nucleic Acids Res. 2011 Jan;39(Database issue):D456-64. doi: 10.1093/nar/gkq880. Epub 2010 Oct 8.

12.

Macromolecular docking restrained by a small angle X-ray scattering profile.

Schneidman-Duhovny D, Hammel M, Sali A.

J Struct Biol. 2011 Mar;173(3):461-71. doi: 10.1016/j.jsb.2010.09.023. Epub 2010 Oct 12.

13.

3-D structures of macromolecules using single-particle analysis in EMAN.

Ludtke SJ.

Methods Mol Biol. 2010;673:157-73. doi: 10.1007/978-1-60761-842-3_9.

PMID:
20835797
14.

Determining macromolecular assembly structures by molecular docking and fitting into an electron density map.

Lasker K, Sali A, Wolfson HJ.

Proteins. 2010 Nov 15;78(15):3205-11. doi: 10.1002/prot.22845.

15.

The nuclear pore complex and nuclear transport.

Wente SR, Rout MP.

Cold Spring Harb Perspect Biol. 2010 Oct;2(10):a000562. doi: 10.1101/cshperspect.a000562. Epub 2010 Jul 14. Review.

16.

Integrative structure modeling of macromolecular assemblies from proteomics data.

Lasker K, Phillips JL, Russel D, Velázquez-Muriel J, Schneidman-Duhovny D, Tjioe E, Webb B, Schlessinger A, Sali A.

Mol Cell Proteomics. 2010 Aug;9(8):1689-702. doi: 10.1074/mcp.R110.000067. Epub 2010 May 27.

17.

FoXS: a web server for rapid computation and fitting of SAXS profiles.

Schneidman-Duhovny D, Hammel M, Sali A.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W540-4. doi: 10.1093/nar/gkq461. Epub 2010 May 27.

18.

An efficient protocol for NMR-spectroscopy-based structure determination of protein complexes in solution.

Simon B, Madl T, Mackereth CD, Nilges M, Sattler M.

Angew Chem Int Ed Engl. 2010 Mar 8;49(11):1967-70. doi: 10.1002/anie.200906147. No abstract available.

PMID:
20148424
19.

PHENIX: a comprehensive Python-based system for macromolecular structure solution.

Adams PD, Afonine PV, Bunkóczi G, Chen VB, Davis IW, Echols N, Headd JJ, Hung LW, Kapral GJ, Grosse-Kunstleve RW, McCoy AJ, Moriarty NW, Oeffner R, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Zwart PH.

Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):213-21. doi: 10.1107/S0907444909052925. Epub 2010 Jan 22.

20.

Computer science. Accessible reproducible research.

Mesirov JP.

Science. 2010 Jan 22;327(5964):415-6. doi: 10.1126/science.1179653. No abstract available.

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