PatchDock and SymmDock: servers for rigid and symmetric docking
- D. Schneidman-Duhovny, Y. Inbar, R. Nussinov, H. Wolfson
- Biology, ChemistryNucleic Acids Res.
- 27 June 2005
Two freely available web servers for molecular docking that perform structure prediction of protein–protein and protein–small molecule complexes and the SymmDock method predicts the structure of a homomultimer with cyclic symmetry given theructure of the monomeric unit are described.
Shape complementarity at protein–protein interfaces
A matching algorithm using surface complementarity between receptor and ligand protein molecules is outlined, and it is shown that out of the 16 protein‐protein complexes tried, 15 were successfully docked, including two immunoglobulins.
Efficient Unbound Docking of Rigid Molecules
- D. Schneidman-Duhovny, R. Nussinov, H. Wolfson
- Computer ScienceWorkshop on Algorithms in Bioinformatics
- 17 September 2002
A new algorithm for unbound (real life) docking of molecules, whether protein-protein or protein-drug, carrying out rigid docking, with surface variability/flexibility implicitly addressed through liberal intermolecular penetration is presented.
Geometric Hashing: A General And Efficient Model-based Recognition Scheme
- Y. Lamdan, H. Wolfson
- Computer Science[ Proceedings] Second International Conference on…
- 5 December 1988
A general method for model-based object recognition in occluded scenes is presented based on geometric hashing, which stands out for its efficiency and applications both in 3-D and 2-D.
FireDock: a web server for fast interaction refinement in molecular docking†
- E. Mashiach, D. Schneidman-Duhovny, Nelly Andrusier, R. Nussinov, H. Wolfson
- Computer Science, ChemistryNucleic Acids Res.
- 19 April 2008
The FireDock web server, presented here, is the first web server for flexible refinement and scoring of protein–protein docking solutions and includes optimization of side-chain conformations and rigid-body orientation and allows a high-throughput refinement.
FireDock: Fast interaction refinement in molecular docking
- Nelly Andrusier, R. Nussinov, H. Wolfson
- Computer ScienceProteins: Structure, Function, and Bioinformatics
- 1 October 2007
FireDock's prediction results are comparable to current state‐of‐the‐art refinement methods while its running time is significantly lower, and its refinement procedure significantly improves the ranking of the rigid‐body PatchDock algorithm for these cases.
Context-free attentional operators: The generalized symmetry transform
- D. Reisfeld, H. Wolfson, Y. Yeshurun
- Computer ScienceInternational Journal of Computer Vision
- 1 March 1995
An attention operator based on the intuitive notion of symmetry, which generalized many of the existing methods of detecting regions of interest is presented, a low-level operator that can be applied successfully without a priori knowledge of the world.
Protein structure fitting and refinement guided by cryo-EM density.
A method for simultaneous alignment of multiple protein structures
- Maxim Shatsky, R. Nussinov, H. Wolfson
- Biology, Computer ScienceProteins: Structure, Function, and Bioinformatics
- 1 July 2004
It is their residue sequence order‐independence that allows application of MultiProt to derive multiple alignments of binding sites and of protein‐protein interfaces, making MultiProt an extremely useful structural tool.
Affine invariant model-based object recognition
An efficient matching algorithm, which assumes affine approximation to the prospective viewing transformation, is proposed and was successfully tested in recognition of industrial objects appearing in composite occluded scenes.