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Results: 1 to 20 of 38

1.

Uncertainty in integrative structural modeling.

Schneidman-Duhovny D, Pellarin R, Sali A.

Curr Opin Struct Biol. 2014 Aug 27;28C:96-104. doi: 10.1016/j.sbi.2014.08.001. [Epub ahead of print] Review.

PMID:
25173450
[PubMed - as supplied by publisher]
2.

Molecular architecture of photoreceptor phosphodiesterase elucidated by chemical cross-linking and integrative modeling.

Zeng-Elmore X, Gao XZ, Pellarin R, Schneidman-Duhovny D, Zhang XJ, Kozacka KA, Tang Y, Sali A, Chalkley RJ, Cote RH, Chu F.

J Mol Biol. 2014 Aug 19. pii: S0022-2836(14)00425-2. doi: 10.1016/j.jmb.2014.07.033. [Epub ahead of print]

PMID:
25149264
[PubMed - as supplied by publisher]
3.

SAXS Merge: an automated statistical method to merge SAXS profiles using Gaussian processes.

Spill YG, Kim SJ, Schneidman-Duhovny D, Russel D, Webb B, Sali A, Nilges M.

J Synchrotron Radiat. 2014 Jan;21(Pt 1):203-8. doi: 10.1107/S1600577513030117. Epub 2013 Dec 14.

PMID:
24365937
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

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

Pieper U, Webb BM, Dong GQ, Schneidman-Duhovny D, Fan H, Kim SJ, Khuri N, Spill YG, Weinkam P, Hammel M, Tainer JA, Nilges M, Sali A.

Nucleic Acids Res. 2014 Jan;42(Database issue):D336-46. doi: 10.1093/nar/gkt1144. Epub 2013 Nov 23.

PMID:
24271400
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Modeling of proteins and their assemblies with the Integrative Modeling Platform.

Webb B, Lasker K, Velázquez-Muriel J, Schneidman-Duhovny D, Pellarin R, Bonomi M, Greenberg C, Raveh B, Tjioe E, Russel D, Sali A.

Methods Mol Biol. 2014;1091:277-95. doi: 10.1007/978-1-62703-691-7_20.

PMID:
24203340
[PubMed - indexed for MEDLINE]
6.

Recovering a representative conformational ensemble from underdetermined macromolecular structural data.

Berlin K, Castañeda CA, Schneidman-Duhovny D, Sali A, Nava-Tudela A, Fushman D.

J Am Chem Soc. 2013 Nov 6;135(44):16595-609.

PMID:
24093873
[PubMed - in process]
7.

Optimized atomic statistical potentials: assessment of protein interfaces and loops.

Dong GQ, Fan H, Schneidman-Duhovny D, Webb B, Sali A.

Bioinformatics. 2013 Dec 15;29(24):3158-66. doi: 10.1093/bioinformatics/btt560. Epub 2013 Sep 27.

PMID:
24078704
[PubMed - indexed for MEDLINE]
8.

Accurate SAXS profile computation and its assessment by contrast variation experiments.

Schneidman-Duhovny D, Hammel M, Tainer JA, Sali A.

Biophys J. 2013 Aug 20;105(4):962-74. doi: 10.1016/j.bpj.2013.07.020.

PMID:
23972848
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Assembly of macromolecular complexes by satisfaction of spatial restraints from electron microscopy images.

Velázquez-Muriel J, Lasker K, Russel D, Phillips J, Webb BM, Schneidman-Duhovny D, Sali A.

Proc Natl Acad Sci U S A. 2012 Nov 13;109(46):18821-6. doi: 10.1073/pnas.1216549109. Epub 2012 Oct 29.

PMID:
23112201
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

A method for integrative structure determination of protein-protein complexes.

Schneidman-Duhovny D, Rossi A, Avila-Sakar A, Kim SJ, Velázquez-Muriel J, Strop P, Liang H, Krukenberg KA, Liao M, Kim HM, Sobhanifar S, Dötsch V, Rajpal A, Pons J, Agard DA, Cheng Y, Sali A.

Bioinformatics. 2012 Dec 15;28(24):3282-9. doi: 10.1093/bioinformatics/bts628. Epub 2012 Oct 23.

PMID:
23093611
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Integrative structural modeling with small angle X-ray scattering profiles.

Schneidman-Duhovny D, Kim SJ, Sali A.

BMC Struct Biol. 2012 Jul 16;12:17. doi: 10.1186/1472-6807-12-17. Review.

PMID:
22800408
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Putting the pieces together: integrative modeling platform software for structure determination of macromolecular assemblies.

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

PLoS Biol. 2012 Jan;10(1):e1001244. doi: 10.1371/journal.pbio.1001244. Epub 2012 Jan 17.

PMID:
22272186
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Statistical potential for modeling and ranking of protein-ligand interactions.

Fan H, Schneidman-Duhovny D, Irwin JJ, Dong G, Shoichet BK, Sali A.

J Chem Inf Model. 2011 Dec 27;51(12):3078-92. doi: 10.1021/ci200377u. Epub 2011 Nov 21.

PMID:
22014038
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

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.

PMID:
21963794
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Modeling of proteins and their assemblies with the integrative modeling platform.

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

Methods Mol Biol. 2011;781:377-97. doi: 10.1007/978-1-61779-276-2_19.

PMID:
21877292
[PubMed - indexed for MEDLINE]
16.

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.

PMID:
21097780
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

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.

PMID:
20920583
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

An integrated suite of fast docking algorithms.

Mashiach E, Schneidman-Duhovny D, Peri A, Shavit Y, Nussinov R, Wolfson HJ.

Proteins. 2010 Nov 15;78(15):3197-204. doi: 10.1002/prot.22790.

PMID:
20607855
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

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.

PMID:
20507923
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

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.

PMID:
20507903
[PubMed - indexed for MEDLINE]
Free PMC Article

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