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Items: 1 to 20 of 45

1.

Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment.

Lensink MF, Velankar S, Kryshtafovych A, Huang SY, Schneidman-Duhovny D, Sali A, Segura J, Fernandez-Fuentes N, Viswanath S, Elber R, Grudinin S, Popov P, Neveu E, Lee H, Baek M, Park S, Heo L, Rie Lee G, Seok C, Qin S, Zhou HX, Ritchie DW, Maigret B, Devignes MD, Ghoorah A, Torchala M, Chaleil RA, Bates PA, Ben-Zeev E, Eisenstein M, Negi SS, Weng Z, Vreven T, Pierce BG, Borrman TM, Yu J, Ochsenbein F, Guerois R, Vangone A, Rodrigues JP, van Zundert G, Nellen M, Xue L, Karaca E, Melquiond AS, Visscher K, Kastritis PL, Bonvin AM, Xu X, Qiu L, Yan C, Li J, Ma Z, Cheng J, Zou X, Shen Y, Peterson LX, Kim HR, Roy A, Han X, Esquivel-Rodriguez J, Kihara D, Yu X, Bruce NJ, Fuller JC, Wade RC, Anishchenko I, Kundrotas PJ, Vakser IA, Imai K, Yamada K, Oda T, Nakamura T, Tomii K, Pallara C, Romero-Durana M, Jiménez-García B, Moal IH, Férnandez-Recio J, Joung JY, Kim JY, Joo K, Lee J, Kozakov D, Vajda S, Mottarella S, Hall DR, Beglov D, Mamonov A, Xia B, Bohnuud T, Del Carpio CA, Ichiishi E, Marze N, Kuroda D, Roy Burman SS, Gray JJ, Chermak E, Cavallo L, Oliva R, Tovchigrechko A, Wodak SJ.

Proteins. 2016 Apr 28. doi: 10.1002/prot.25007. [Epub ahead of print]

PMID:
27122118
2.

Expansion of phenotype and genotypic data in CRB2-related syndrome.

Lamont RE, Tan WH, Innes AM, Parboosingh JS, Schneidman-Duhovny D, Rajkovic A, Pappas J, Altschwager P, DeWard S, Fulton A, Gray KJ, Krall M, Mehta L, Rodan LH, Saller DN Jr, Steele D, Stein D, Yatsenko SA, Bernier FP, Slavotinek AM.

Eur J Hum Genet. 2016 Mar 23. doi: 10.1038/ejhg.2016.24. [Epub ahead of print]

PMID:
27004616
3.

CryptoSite: Expanding the Druggable Proteome by Characterization and Prediction of Cryptic Binding Sites.

Cimermancic P, Weinkam P, Rettenmaier TJ, Bichmann L, Keedy DA, Woldeyes RA, Schneidman-Duhovny D, Demerdash ON, Mitchell JC, Wells JA, Fraser JS, Sali A.

J Mol Biol. 2016 Feb 22;428(4):709-19. doi: 10.1016/j.jmb.2016.01.029. Epub 2016 Feb 5.

PMID:
26854760
4.

DksA regulates RNA polymerase in Escherichia coli through a network of interactions in the secondary channel that includes Sequence Insertion 1.

Parshin A, Shiver AL, Lee J, Ozerova M, Schneidman-Duhovny D, Gross CA, Borukhov S.

Proc Natl Acad Sci U S A. 2015 Dec 15;112(50):E6862-71. doi: 10.1073/pnas.1521365112. Epub 2015 Nov 24. Erratum in: Proc Natl Acad Sci U S A. 2016 Jan 5;113(1):E103.

PMID:
26604313
5.

Prion Protein-Antibody Complexes Characterized by Chromatography-Coupled Small-Angle X-Ray Scattering.

Carter L, Kim SJ, Schneidman-Duhovny D, Stöhr J, Poncet-Montange G, Weiss TM, Tsuruta H, Prusiner SB, Sali A.

Biophys J. 2015 Aug 18;109(4):793-805. doi: 10.1016/j.bpj.2015.06.065.

PMID:
26287631
6.

CRB2 mutations produce a phenotype resembling congenital nephrosis, Finnish type, with cerebral ventriculomegaly and raised alpha-fetoprotein.

Slavotinek A, Kaylor J, Pierce H, Cahr M, DeWard SJ, Schneidman-Duhovny D, Alsadah A, Salem F, Schmajuk G, Mehta L.

Am J Hum Genet. 2015 Jan 8;96(1):162-9. doi: 10.1016/j.ajhg.2014.11.013. Epub 2014 Dec 31.

7.

Uncertainty in integrative structural modeling.

Schneidman-Duhovny D, Pellarin R, Sali A.

Curr Opin Struct Biol. 2014 Oct;28:96-104. doi: 10.1016/j.sbi.2014.08.001. Epub 2014 Aug 28. Review.

8.

Structural characterization by cross-linking reveals the detailed architecture of a coatomer-related heptameric module from the nuclear pore complex.

Shi Y, Fernandez-Martinez J, Tjioe E, Pellarin R, Kim SJ, Williams R, Schneidman-Duhovny D, Sali A, Rout MP, Chait BT.

Mol Cell Proteomics. 2014 Nov;13(11):2927-43. doi: 10.1074/mcp.M114.041673. Epub 2014 Aug 26.

9.

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 Nov 11;426(22):3713-28. doi: 10.1016/j.jmb.2014.07.033. Epub 2014 Aug 19.

10.

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.

11.

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.

12.

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
13.

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.

14.

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.

15.

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.

16.

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.

17.

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.

18.

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.

19.

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.

20.

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.

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