Dina Schneidman

Research Publications Software

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

Research Interests

  • Structural characterization of protein assemblies using Small Angle X-ray scattering (SAXS)
  • Simulating the dynamics of protein folding
  • Prediction of structures of antibody-antigen interactions

Publications

  • 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.
  • 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.
  • 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 ]

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