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Items: 1 to 50 of 57

1.

Integrative Structure Modeling: Overview and Assessment.

Braitbard M, Schneidman-Duhovny D, Kalisman N.

Annu Rev Biochem. 2019 Jun 20;88:113-135. doi: 10.1146/annurev-biochem-013118-111429. Epub 2019 Mar 4.

PMID:
30830798
2.

Biallelic sequence variants in INTS1 in patients with developmental delays, cataracts, and craniofacial anomalies.

Krall M, Htun S, Schnur RE, Brooks AS, Baker L, de Alba Campomanes A, Lamont RE, Gripp KW; Care 4 Rare Canada Consortium, Schneidman-Duhovny D, Innes AM, Mancini GMS, Slavotinek AM.

Eur J Hum Genet. 2019 Apr;27(4):582-593. doi: 10.1038/s41431-018-0298-9. Epub 2019 Jan 8.

PMID:
30622326
3.

Predicting CD4 T-cell epitopes based on antigen cleavage, MHCII presentation, and TCR recognition.

Schneidman-Duhovny D, Khuri N, Dong GQ, Winter MB, Shifrut E, Friedman N, Craik CS, Pratt KP, Paz P, Aswad F, Sali A.

PLoS One. 2018 Nov 6;13(11):e0206654. doi: 10.1371/journal.pone.0206654. eCollection 2018.

4.

Modeling Structure and Dynamics of Protein Complexes with SAXS Profiles.

Schneidman-Duhovny D, Hammel M.

Methods Mol Biol. 2018;1764:449-473. doi: 10.1007/978-1-4939-7759-8_29.

5.

De novo, deleterious sequence variants that alter the transcriptional activity of the homeoprotein PBX1 are associated with intellectual disability and pleiotropic developmental defects.

Slavotinek A, Risolino M, Losa M, Cho MT, Monaghan KG, Schneidman-Duhovny D, Parisotto S, Herkert JC, Stegmann APA, Miller K, Shur N, Chui J, Muller E, DeBrosse S, Szot JO, Chapman G, Pachter NS, Winlaw DS, Mendelsohn BA, Dalton J, Sarafoglou K, Karachunski PI, Lewis JM, Pedro H, Dunwoodie SL, Selleri L, Shieh J.

Hum Mol Genet. 2017 Dec 15;26(24):4849-4860. doi: 10.1093/hmg/ddx363.

6.

Cross-activating c-Met/β1 integrin complex drives metastasis and invasive resistance in cancer.

Jahangiri A, Nguyen A, Chandra A, Sidorov MK, Yagnik G, Rick J, Han SW, Chen W, Flanigan PM, Schneidman-Duhovny D, Mascharak S, De Lay M, Imber B, Park CC, Matsumoto K, Lu K, Bergers G, Sali A, Weiss WA, Aghi MK.

Proc Natl Acad Sci U S A. 2017 Oct 10;114(41):E8685-E8694. doi: 10.1073/pnas.1701821114. Epub 2017 Sep 26.

7.

2017 publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution: an update.

Trewhella J, Duff AP, Durand D, Gabel F, Guss JM, Hendrickson WA, Hura GL, Jacques DA, Kirby NM, Kwan AH, Pérez J, Pollack L, Ryan TM, Sali A, Schneidman-Duhovny D, Schwede T, Svergun DI, Sugiyama M, Tainer JA, Vachette P, Westbrook J, Whitten AE.

Acta Crystallogr D Struct Biol. 2017 Sep 1;73(Pt 9):710-728. doi: 10.1107/S2059798317011597. Epub 2017 Aug 18.

8.

Reconstruction of 3D structures of MET antibodies from electron microscopy 2D class averages.

Chen Q, Vieth M, Timm DE, Humblet C, Schneidman-Duhovny D, Chemmama IE, Sali A, Zeng W, Lu J, Liu L.

PLoS One. 2017 Apr 13;12(4):e0175758. doi: 10.1371/journal.pone.0175758. eCollection 2017.

9.

Formation of a repressive complex in the mammalian circadian clock is mediated by the secondary pocket of CRY1.

Michael AK, Fribourgh JL, Chelliah Y, Sandate CR, Hura GL, Schneidman-Duhovny D, Tripathi SM, Takahashi JS, Partch CL.

Proc Natl Acad Sci U S A. 2017 Feb 14;114(7):1560-1565. doi: 10.1073/pnas.1615310114. Epub 2017 Jan 31.

10.

Insights into HIV-1 proviral transcription from integrative structure and dynamics of the Tat:AFF4:P-TEFb:TAR complex.

Schulze-Gahmen U, Echeverria I, Stjepanovic G, Bai Y, Lu H, Schneidman-Duhovny D, Doudna JA, Zhou Q, Sali A, Hurley JH.

Elife. 2016 Oct 12;5. pii: e15910. doi: 10.7554/eLife.15910.

11.

Memdock: an α-helical membrane protein docking algorithm.

Hurwitz N, Schneidman-Duhovny D, Wolfson HJ.

Bioinformatics. 2016 Aug 15;32(16):2444-50. doi: 10.1093/bioinformatics/btw184. Epub 2016 Apr 8.

PMID:
27153621
12.

FoXS, FoXSDock and MultiFoXS: Single-state and multi-state structural modeling of proteins and their complexes based on SAXS profiles.

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

Nucleic Acids Res. 2016 Jul 8;44(W1):W424-9. doi: 10.1093/nar/gkw389. Epub 2016 May 5.

13.

Prediction of homoprotein and heteroprotein 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 Sep;84 Suppl 1:323-48. doi: 10.1002/prot.25007. Epub 2016 Jun 1.

14.

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 Oct;24(10):1436-44. doi: 10.1038/ejhg.2016.24. Epub 2016 Mar 23. Review.

15.

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):709-719. doi: 10.1016/j.jmb.2016.01.029. Epub 2016 Feb 5.

16.

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.

17.

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.

18.

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.

19.

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.

20.

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.

21.

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):3713-3728. doi: 10.1016/j.jmb.2014.07.033. Epub 2014 Aug 19.

22.

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.

23.

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.

24.

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
25.

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.

26.

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.

27.

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.

28.

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.

29.

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.

30.

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.

31.

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.

32.

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.

33.

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.

34.

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
35.

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.

36.

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.

37.

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.

38.

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.

39.

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.

40.

Novel approach for efficient pharmacophore-based virtual screening: method and applications.

Dror O, Schneidman-Duhovny D, Inbar Y, Nussinov R, Wolfson HJ.

J Chem Inf Model. 2009 Oct;49(10):2333-43. doi: 10.1021/ci900263d.

41.

The structural dynamics of macromolecular processes.

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

Curr Opin Cell Biol. 2009 Feb;21(1):97-108. doi: 10.1016/j.ceb.2009.01.022. Epub 2009 Feb 14. Review.

42.

Structural similarity of genetically interacting proteins.

Dror O, Schneidman-Duhovny D, Shulman-Peleg A, Nussinov R, Wolfson HJ, Sharan R.

BMC Syst Biol. 2008 Jul 31;2:69. doi: 10.1186/1752-0509-2-69.

43.

Deterministic pharmacophore detection via multiple flexible alignment of drug-like molecules.

Schneidman-Duhovny D, Dror O, Inbar Y, Nussinov R, Wolfson HJ.

J Comput Biol. 2008 Sep;15(7):737-54. doi: 10.1089/cmb.2007.0130.

44.

PharmaGist: a webserver for ligand-based pharmacophore detection.

Schneidman-Duhovny D, Dror O, Inbar Y, Nussinov R, Wolfson HJ.

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W223-8. doi: 10.1093/nar/gkn187. Epub 2008 Apr 19.

45.

FireDock: a web server for fast interaction refinement in molecular docking.

Mashiach E, Schneidman-Duhovny D, Andrusier N, Nussinov R, Wolfson HJ.

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W229-32. doi: 10.1093/nar/gkn186. Epub 2008 Apr 19.

46.

Metabolic stereoselectivity of cytochrome P450 3A4 towards deoxypodophyllotoxin: In silico predictions and experimental validation.

Julsing MK, Vasilev NP, Schneidman-Duhovny D, Muntendam R, Woerdenbag HJ, Quax WJ, Wolfson HJ, Ionkova I, Kayser O.

Eur J Med Chem. 2008 Jun;43(6):1171-9. Epub 2007 Sep 19.

PMID:
17998150
47.

Automatic prediction of protein interactions with large scale motion.

Schneidman-Duhovny D, Nussinov R, Wolfson HJ.

Proteins. 2007 Dec 1;69(4):764-73.

PMID:
17886339
48.

HingeProt: automated prediction of hinges in protein structures.

Emekli U, Schneidman-Duhovny D, Wolfson HJ, Nussinov R, Haliloglu T.

Proteins. 2008 Mar;70(4):1219-27.

PMID:
17847101
49.

Mechanism of two classes of cancer mutations in the phosphoinositide 3-kinase catalytic subunit.

Miled N, Yan Y, Hon WC, Perisic O, Zvelebil M, Inbar Y, Schneidman-Duhovny D, Wolfson HJ, Backer JM, Williams RL.

Science. 2007 Jul 13;317(5835):239-42.

50.

Geometry-based flexible and symmetric protein docking.

Schneidman-Duhovny D, Inbar Y, Nussinov R, Wolfson HJ.

Proteins. 2005 Aug 1;60(2):224-31.

PMID:
15981269

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