Dina Schneidman

Postdoc at Sali lab at UCSF

Office address:
Mission Bay, Byers Hall 1700 4th Street,
University of California, San Francisco
San Francisco, CA 94158

Email: dina at salilab.org

Computational Structural Biology, Structural Bioinformatics, Small Angle X-ray Scattering (SAXS), B-cell and T-cell epitope prediction

Research Interests

  • Integrative modeling of protein-protein interactions. While in most of the cases docking algorithms can sample the near-native structure of the complex, ranking it among the top scoring ones remains a challenge. Integrative docking approach computationally integrates data from a variety of fast and accessible experimental techniques, such as small angle X-ray scattering, 2D and 3D electron microscopy, cross linking detected by mass spectrometry, and fast interface mapping by NMR, for rapid and accurate structure determination of protein-protein complexes.
  • Conformational heterogeneity from SAXS profiles. SAXS profiles, while limited in resolution, contain shape information about conformational and compositional states of the system. Moreover, SAXS datasets can be rapidly collected for a range of solution conditions, such as addition of a ligand, different temperatures, or pH values. Given a set of multiple SAXS profiles and one or more input structure we can simultaneously uncover the set of structural states that exist across all input samples as well as their population weights in each sample.
  • Prediction of structures of antibody-antigen interactions from SAXS profiles.
  • Modeling of antigen processing, MHCII presentation and T-cell recognition for T-cell epitope prediction.
  • Computational methods for drug discovery: docking, B-cell and T-cell epitope prediction, pharmacophore detection and virtual screening.

Publications

Scholar profile
  • Schneidman-Duhovny D, Pellarin R, Sali A. Uncertainty in integrative structural modeling. Curr Opin Struct Biol. 28, 96-104, 2014 [ Abstract ]
  • Shi Y, Fernandez-Martinez J, Tjioe E, Pellarin R, Kim SJ, Williams R, Schneidman-Duhovny D, Sali A, Rout MP, Chait BT. Structural characterization by cross-linking reveals the detailed architecture of a coatomer-related heptameric module from the nuclear pore complex. Mol Cell Proteomics. 2014
  • Zeng-Elmore X, Gao XZ, Pellarin R, Schneidman-Duhovny D, Zhang XJ, Kozacka KA, Tang Y, Sali A, Chalkley RJ, Cote RH, Chu F. Molecular architecture of photoreceptor phosphodiesterase elucidated by chemical cross-linking and integrative modeling. J Mol Biol. 2014
  • 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. ModBase, a database of annotated comparative protein structure models and associated resources. Nucleic Acids Res. 42:D336-46, 2014
  • Webb B, Lasker K, Velázquez-Muriel J, Schneidman-Duhovny D, Pellarin R, Bonomi M, Greenberg C, Raveh B, Tjioe E, Russel D, Sali A. Modeling of proteins and their assemblies with the Integrative Modeling Platform. Methods Mol Biol. 1091:277-95, 2014
  • Spill YG, Kim SJ, Schneidman-Duhovny D, Russel D, Webb B, Sali A, Nilges M. SAXS Merge: an automated statistical method to merge SAXS profiles using Gaussian processes. J Synchrotron Radiat. 21:203-8, 2014
  • Berlin K, Castañeda CA, Schneidman-Duhovny D, Sali A, Nava-Tudela A, Fushman D. Recovering a representative conformational ensemble from underdetermined macromolecular structural data. J Am Chem Soc. 135:16595-609, 2013
  • Dong GQ, Fan H, Schneidman-Duhovny D, Webb B, Sali A. Optimized atomic statistical potentials: assessment of protein interfaces and loops. Bioinformatics. 29:3158-66, 2013
  • Schneidman-Duhovny D, Hammel M, Tainer JA, Sali A. Accurate SAXS profile computation and its assessment by contrast variation experiments. Biophysical Journal, 105:962-74, 2013 [ FREE Full Text ]
  • Schneidman-Duhovny D, Rossi A, Avila-Sakar A, Kim SJ, Velázquez-Muriel J, Strop P, Liang H, Krukenberg K, Liao M, Kim HM, Sobhanifar S, Dötsch V, Rajpal A, Pons J, Agard DA, Cheng Y, Sali A. A method for integrative structure determination of protein-protein complexes. Bioinformatics, 28(24):3282-9, 2012 [ Abstract ] [ PDF ]
  • Schneidman-Duhovny D, Kim SJ, Sali A. Integrative structural modeling with small angle X-ray scattering profiles. BMC Struct Biol. 12:17, 2012 [ FREE Full Text ]
  • Russel D, Lasker K, Webb B, Velázquez-Muriel J, Tjioe E, Schneidman-Duhovny D, Peterson B, Sali A. Putting the pieces together: integrative modeling platform software for structure determination of macromolecular assemblies. PLoS Biol. 10:e1001244, 2012 [ FREE Full Text ]
  • Fan H, Schneidman-Duhovny D, Irwin JJ, Dong G, Shoichet BK, Sali A. Statistical potential for modeling and ranking of protein-ligand interactions. J Chem Inf Model. 51:3078-92, 2011 [ Abstract ]
  • Yang Z, Lasker K, Schneidman-Duhovny D, Webb B, Huang CC, Pettersen EF, Goddard TD, Meng EC, Sali A, Ferrin TE. UCSF Chimera, MODELLER, and IMP: An integrated modeling system. J Struct Biol. 179:269 278, 2011 [ Abstract ]
  • Webb B, Lasker K, Schneidman-Duhovny D, Tjioe E, Phillips J, Kim SJ, Velázquez-Muriel J, Russel D, Sali A. Modeling of proteins and their assemblies with the integrative modeling platform. Methods Mol Biol. 781:377-97, 2011 [ Abstract ]
  • 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. ModBase, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res. 39 Suppl:D465-74, 2011 [ FREE Full Text ]
  • Schneidman-Duhovny D, Hammel M, Sali A. Macromolecular docking restrained by a small angle X-ray scattering profile. J Struct Biol. 173:461 471, 2011 [ Abstract ]
  • Mashiach E, Schneidman-Duhovny D, Peri A, Shavit Y, Nussinov R, Wolfson HJ. An integrated suite of fast docking algorithms. Proteins. 78(15):3197-204, 2010. [ Abstract ]
  • Schneidman-Duhovny D, Hammel M, Sali A. FoXS: a web server for rapid computation and fitting of SAXS profiles. Nucleic Acids Res. 38 Suppl:W540-4, 2010. [ FREE Full Text ]
  • Lasker K, Phillips JL, Russel D, Velazquez-Muriel J, Schneidman-Duhovny D, Tjioe E, Webb B, Schlessinger A, Sali A. Integrative structure modeling of macromolecular assemblies from proteomics data. Mol Cell Proteomics. 2010.
  • Dror O, Schneidman-Duhovny D,Inbar Y, Nussinov R, Wolfson HJ. Novel Approach for Efficient Pharmacophore-Based Virtual Screening: Method and Applications. J Chem Inf Model. 49(10):2333-43, 2009. [ Abstract ]
  • Russel D, Lasker K, Phillips J, Schneidman-Duhovny D, Velázquez-Muriel JA, Sali A. The structural dynamics of macromolecular processes. Curr Opin Cell Biol. 21(1):97-108, 2009 [ FREE Full Text ]
  • Dror O, Schneidman-Duhovny D, Shulman-Peleg A, Nussinov R, Wolfson HJ, Sharan R. Structural similarity of genetically interacting proteins. BMC Syst Biol. 31;2:69, 2008. [ FREE Full Text ]
  • Schneidman-Duhovny D, Dror O, Inbar Y, Nussinov R, Wolfson HJ. Deterministic pharmacophore detection via multiple flexible alignment of drug-like molecules. J Comput Biol. 15:737-54, 2008. [ FREE Full Text ]
  • Schneidman-Duhovny D, Dror O, Inbar Y, Nussinov R, Wolfson HJ. PharmaGist: a webserver for ligand-based pharmacophore detection. Nucleic Acids Research 2008. [Abstract ]
  • Mashiach E, Schneidman-Duhovny D, Andrusier N, Nussinov R, Wolfson HJ. FireDock: a web server for fast interaction refinement in molecular docking. Nucleic Acids Res. 2008 [Abstract ]
  • Julsing MK, Vasilev NP, Schneidman-Duhovny D, Muntendam R, Woerdenbag HJ, Quax WJ, Wolfson HJ, Ionkova I, Kayser O. Metabolic stereoselectivity of cytochrome P450 3A4 towards deoxypodophyllotoxin: in silico predictions and experimental validation. European Journal of Medicinal Chemistry [Abstract ]
  • Emekli U, Schneidman-Duhovny D, Wolfson HJ, Nussinov R, Haliloglu T. HingeProt: Automated Prediction of Hinges in Protein Structures. Proteins 70:1219-27, 2008. [Abstract ]
  • Schneidman-Duhovny D, Nussinov R, Wolfson HJ. Automatic prediction of protein interactions with large scale motion. Proteins (CAPRI issue) 69:764-773, 2007. [Abstract ]
  • Miled N, Yan Y, Hon W, Perisic O, Zvelebil M, Inbar Y, Schneidman-Duhovny D, Wolfson HJ, Backer JM, Williams RL. Mechanism of two classes of cancer mutations in the phosphoinositide 3-kinase catalytic subunit. Science 317:239-242, 2007. [Abstract ]
  • Inbar Y, Schneidman-Duhovny D, Dror O, Nussinov R, Wolfson HJ. Deterministic Pharmacophore Detection via Multiple Flexible Alignment of Drug-Like Molecules. In Proc. of RECOMB 2007, vol. 3692 of Lecture Notes in Computer Science, pp. 423-434. Springer Verlag.
  • Schneidman-Duhovny D,Nussinov R, Wolfson HJ. Predicting molecular interactions in silico II: protein-protein and protein-drug docking. Frontiers Med. Chem. 3, 585-613, 2006.
  • Schneidman-Duhovny D, Inbar Y, Nussinov R, Wolfson HJ. PatchDock and SymmDock: servers for rigid and symmetric docking. NAR, 33: W363-W367, 2005. [Abstract ] [ FREE Full Text ]
  • Schneidman-Duhovny D, Inbar Y, Nussinov R, Wolfson HJ. Geometry based flexible protein docking. Proteins, 60: 224-231, 2005. [Abstract ]
  • Inbar Y, Schneidman-Duhovny D, Halperin I, Oron A, Nussinov R, Wolfson HJ. Approaching the CAPRI Challenge with Efficient Geometry Based Docking. Proteins 60: 217-223, 2005. [Abstract ]
  • Wolfson HJ, Shatsky M, Schneidman-Duhovny D, Dror O, Shulman-Peleg A, Ma B, Nussinov R. From structure to function: methods and applications. Curr. Prot. and Peptide Sci. 6: 171-83, 2005.
  • Shatsky M, Dror O, Schneidman-Duhovny D, Nussinov R, Wolfson HJ. BioInfo3D: a suite of tools for structural bioinformatics Nucl. Acids. Res. 32: W503-W507, 2004. [ Abstract ] [ FREE Full Text ]
  • Gidalevitz T, Biswas C, Ding H, Schneidman-Duhovny D, Wolfson HJ, Stevens F, Radford S, Argon Y. Identification of the N-terminal peptide binding site of glucose-regulated protein 94. J Biol Chem. 279(16):16543-52, 2004. [ Abstract ] [ PDF file ]
  • Schneidman-Duhovny D,Nussinov R, Wolfson HJ. Predicting molecular interactions in silico II: protein-protein and protein-drug docking. Curr. Med. Chem. 11(1): 91-107, 2004. [ Abstract ]
  • Schneidman-Duhovny D, Inbar Y, Polak V, Shatsky M, Halperin I, Benyamini H, Barzilai A, Dror O, Haspel N, Nussinov R, Wolfson HJ. Taking geometry to its edge: fast unbound rigid (and hinge-bent) docking. Proteins. 52(1): 107-12, 2003. [ Abstract ] [ PDF file ]
  • Duhovny D, Nussinov R, Wolfson HJ. Efficient Unbound Docking of Rigid Molecules. In Gusfield et al., Ed. Proceedings of the 2'nd Workshop on Algorithms in Bioinformatics(WABI) Rome, Italy, Lecture Notes in Computer Science 2452, pp. 185-200, Springer Verlag, 2002 [ PDF file ]

Software

  • PatchDock server - a method for fast rigid unbound docking of molecules.
  • FireDock server - an efficient method for refinement and re-scoring of rigid-body protein-protein docking solutions.
  • SymmDock server - a method for prediction of complexes with Cn symmetry by geometry based docking.
  • HingeProt server - a method for protein hinge prediction using Normal Mode Analysis.
  • FlexDock - a method for docking with large scale motion.
  • PharmaGist - a freely available web server for pharmacophore detection.
  • FoXS - a server for fast SAXS profile computation with Debye formula.
  • FoXSDock - a server for docking with SAXS profiles.
  • IMP - Integrative Modeling Platform.