Publications

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Contents

List of publications

Articles

  1. V.D. Milman, H. Wolfson, Minkowski Spaces with Extremal Distance from the Euclidean 'Space', Israel J. of Math.29 (2-3), 113--131, (1978).
  2. J. Bourgain, V. Milman, H. Wolfson, On Type of Metric Spaces, Transactions of the American Math. Soc., 294(1), 295--317, (1986).
  3. H. Wolfson, E. Schonberg, A. Kalvin, Y. Lamdan, Solving Jigsaw Puzzles by Computer Vision, Annals of Operations Research, 12, 51--64, (1988).
  4. G. Burdea, H.J. Wolfson, Solving Jigsaw Puzzles by a Robot, IEEE Transactions on Robotics and Automation 5(6), 752--764, (1989).
  5. H.J. Wolfson, On Curve Matching, IEEE Transactions on Pattern Analysis and Machine Intelligence, 12(5), 483--489, (1990).
  6. Y. Lamdan, J.T. Schwartz, H.J. Wolfson, Affine Invariant Model-Based Object Recognition, IEEE Transactions on Robotics and Automation, 6(5), 578--589, (1990).
  7. E. Kishon, T. Hastie, H. Wolfson, 3-D Curve Matching using Splines, J. of Robotic Systems 8(6), 723-743, (1991).
  8. H.J. Wolfson, Generalizing the Generalized Hough Transform, Pattern Recognition Letters 12(9), 565-573, (1991).
  9. R. Nussinov, H.J. Wolfson, Efficient Detection of Three – Dimensional Motifs in Biological Macromolecules by Computer Vision Techniques, Proceedings of the National Academy of Sciences, U.S.A., 88, 10495-10499, (1991).
  10. E. Sali, H. Wolfson, Texture Classification in Aerial Photographs and Satellite Data, Int. J. on Remote Sensing 13:18, 3395-3408, (1992).
  11. D. Fischer, O. Bachar, R. Nussinov, H.J. Wolfson, An Efficient Automated Computer Vision Based Technique for Detection of Three Dimensional Structural Motifs in Proteins, J. of Biomolecular Structure and Dynamics, 9(4), 769-789, (1992).
  12. O. Bachar, D. Fischer, R. Nussinov, H.J. Wolfson, A Computer Vision Based Technique for 3-D Sequence-Independent Structural Comparison of Proteins, Protein Engineering 6(3), 279-288 (1993).
  13. D. Fischer, R. Norel, H.J. Wolfson, and R. Nussinov, Surface Motifs by a Computer Vision Technique: Searches, Detection and Implications for Protein-Ligand Recognition, PROTEINS: Structure, Function, and Genetics, 16, 278-292, (1993).
  14. D. Fischer, H. Wolfson and R. Nussinov, Spatial, Sequence-Order-Independent Structural Comparison of α/ β Proteins: Evolutionary Implications, J. of Biom. Struct. & Dynamics 11(2), 367-380 (1993).
  15. R. Norel, D. Fischer, H.J. Wolfson and R. Nussinov, Molecular Surface Recognition by a Computer Vision based Technique, Protein Engineering 7, 39-46, (1994).
  16. S. L. Lin, R. Nussinov, D. Fischer, H.J. Wolfson, Molecular Surface Representations by Sparse Critical Points, PROTEINS: Structure, Function, and Genetics, 18, 94-101, (1994).
  17. R. Norel, S. L. Lin, H.J. Wolfson, R. Nussinov, Shape Complementarity at Protein-Protein Interfaces, Biopolymers 34, 933-940 (1994).
  18. D. Fischer, H.J. Wolfson, S. L. Lin, R. Nussinov, Three-dimensional, sequence-order independent Structural Comparison of a Serine Protease against the Crystallographic Database Reveals Active Site Similarities : Potential Implications to Evolution and to Protein Folding, Protein Science 3, 769-778 (1994),
  19. D. Fischer, S.L. Lin, H. J. Wolfson and R. Nussinov, A Geometry-Based Suite of Molecular Docking Processes, Journal of Molecular Biology, 248, 459-477, (1995).
  20. R. Norel, S. L. Lin, H.J. Wolfson, R. Nussinov, Molecular Surface Complementarity at Protein-Protein Interfaces: The Critical Role Played by Surface Normals at Well Placed, Sparse Points in Docking, Journal of Molecular Biology, 252, 263-273, (1995).
  21. D. Reisfeld, H. Wolfson, Y. Yeshurun, Context-Free Attentional Operators: The Generalized Symmetry Transform, Int. J. on Computer Vision, 14(2), 119-130, (1995).
  22. B. Sandak, R. Nussinov, and H.J. Wolfson, An Automated Computer Vision and Robotics-Based Technique for 3-D Flexible Biomolecular Docking and Matching, Computer Applications in the Biosciences (CABIOS), 11(1), 87-99, (1995).
  23. D. Fischer, C.J. Tsai, R. Nussinov and H.J. Wolfson, A 3-D Sequence-Independent Representation of the Protein Databank, Protein Engineering, 8(10), 981-997 (1995).
  24. D. Naor, D. Fischer, R.L. Jernigan, H. J. Wolfson and R. Nussinov, Amino Acid Pair Interchanges at Spatially Conserved Locations, Journal of Molecular Biology, 256 (5), 924-938 (1996).
  25. C.J. Tsai, S.L. Lin, H. J. Wolfson and R. Nussinov, Techniques for Searching for Structural Similarities Between Protein Cores, Protein Surfaces and Between Protein-Protein Interfaces, Techniques in Protein Chemistry, VII, 419-429, (1996).
  26. C.J. Tsai, S.L. Lin, H. J. Wolfson, R. Nussinov, Protein-Protein Interfaces. Architectures and Interactions in Protein-Protein Interfaces and in Protein Cores. Similarities and Differences, Critical Reviews in Biochemistry and Molecular Biology, 31(2), 127-152, (1996).
  27. C.J. Tsai, S.L. Lin, H. J. Wolfson, R. Nussinov, A Dataset of Protein-Protein Interfaces Generated with a Sequence Order Independent Comparison Technique, Journal of Molecular Biology, 260(4), 604-620, (1996).
  28. K.Y. Kupeev and H.J. Wolfson, A New Method of Estimating Shape Similarity, Pattern Recognition Letters, 17, 873-887, (1996).
  29. V. Alesker, R. Nussinov and H. J. Wolfson, Detection of Non-Topological Motifs in Protein Structures, Protein Engineering, 9(12), 1103-1119, (1996).
  30. C.J. Tsai, S.L. Lin, H. J. Wolfson, R. Nussinov, Studies of Protein-Protein Interfaces: A Statistical Analysis of the Hydrophobic Effect, Protein Science, 6, 53-64, (1997).
  31. S.L. Lin, D. Xu, A. Li, M. Rosen, H.J. Wolfson, R. Nussinov, Investigation of the Enzymatic Mechanism of the Yeast Chorismate Mutase by Docking a Transition State Analog, Journal of Molecular Biology, 271(5), 838-845, (1997).
  32. H.J. Wolfson and 'I.' Rigoutsos, Geometric Hashing: An Overview, IEEE Computational Science and Engineering, 4(4), 10-21, (1997).
  33. E. Azarya-Sprinzak, D. Naor, H.J. Wolfson, R. Nussinov, Interchanges of Spatially Neighboring Residues in Structurally Conserved Environments, Protein Engineering, 10(10), 1109-1122, (1997).
  34. M. Rosen, S.L. Lin, H.J. Wolfson and R. Nussinov, Molecular surface comparisons in searches for active sites and functional similarity, Protein Engineering, 11, 263-277, (1998).
  35. B. Sandak, H.J. Wolfson and R. Nussinov, Flexible Docking Allowing Induced Fit in Proteins: Insights From an Open to Closed Conformational Isomers, PROTEINS, 32, 159-174, (1998).
  36. B. Sandak, R. Nussinov, and H.J. Wolfson, A Method for Biomolecular Structural Recognition and Docking Allowing Conformational Flexibility, J. of Computational Biology, 5(4), 631--654, (1998).
  37. G. Verbitsky, R. Nussinov, H.J. Wolfson, Flexible Structural Comparison Allowing Hinge Bending, Swiveling Motions, PROTEINS, 34, 232--254, (1999).
  38. R. Norel, D. Petrey, H.J. Wolfson and R. Nussinov, Examination of Shape Complementarity in Docking of Unbound Proteins, PROTEINS, 36, 307--317, (1999).
  39. R. Norel, H.J. Wolfson and R. Nussinov, Small Molecule Recognition: Solid Angles Surface representation and Molecular Shape Complementarity, Combinatorial Chemistry & High Throughput Screening, 2, 223-236, (1999).
  40. S. Kumar, B. Ma, C.J. Tsai, H.J. Wolfson and R. Nussinov, Folding Funnels and Conformational Transitions via Hinge-Bending Motions, Cell Biochemistry and Biophysics, 31, 141--164, (1999).
  41. R. Nussinov and H.J. Wolfson, Efficient Computational Algorithms for Docking and for Generating and Matching a Library of Epitopes I. Rigid and Flexible Docking Algorithms, Combinatorial Chemistry & High Throughput Screening, vol. 2, 249--259, (1999).
  42. R. Nussinov and H.J. Wolfson, Efficient Computational Algorithms for Docking and for Generating and Matching a Library of Epitopes II: Computer Vision-Based Techniques for the Generation and Utilization of Functional Epitopes, Combinatorial Chemistry & High Throughput Screening, 2, 261--269, (1999).
  43. Z. Hu, B. Ma, H. Wolfson, R. Nussinov, Conservation of Polar Residues as Hot Spots at Protein Interfaces, PROTEINS, 39, 331--342, (2000).
  44. N. Leibowitz, Z.Y. Fligelman, R. Nussinov, H.J. Wolfson, An Automated Multiple Structure Alignment and Detection of a Common Substructural Motif, PROTEINS: Structure, Function and Genetics, 43, 235--245, (2001).
  45. N. Leibowitz, R. Nussinov, H.J. Wolfson, MUSTA - a General, Efficient, Automated Method for Multiple Structure Alignment and Detection of Common Motifs: Application to Proteins, J. of Computational Biology, 8(2), 93--121, (2001).
  46. S. Kumar, H. J. Wolfson and R. Nussinov, Protein Flexibility and Electrostatic Interactions, IBM J. of Research and Development (Special Issue on Deep Computing in the Life Sciences), 43(3-4), 499--512, (2001).
  47. C-J. Tsai, B. Ma, Y.Y. Sham, S. Kumar, H. J. Wolfson and R. Nussinov, A Hierarchical Building-Block-Based Computational Scheme for Protein Structure Prediction, IBM J. of Research and Development (Special Issue on Deep Computing in the Life Sciences), 43(3-4), 513--523, (2001).
  48. B. Ma, H. J. Wolfson and R. Nussinov, Protein Functional Epitopes: Hot Spots, Dynamics and Combinatorial Libraries, Current Opinion in Structural Biology, 11(3), 364--369, (2001).
  49. C-J. Tsai, B. Ma, S. Kumar, H. Wolfson and R. Nussinov, Protein Folding: Binding of Conformationally Fluctuating Building Blocks via Population Selection, Critical Reviews in Biochemistry and Molecular Biology, 36(5), 399-433, (2001).
  50. B. Ma, M. Shatsky, H.J. Wolfson, R. Nussinov, Multiple Diverse Ligands binding at a Single Site: A Matter of Pre-existing Populations, Protein Science, 11, 184-197, (2002).
  51. I. Halperin, B. Ma, H.J. Wolfson and R. Nussinov, Principles of Docking: An Overview of Search Algorithms and a Guide to Scoring Functions, Proteins, 47, 409-443, (2002).
  52. M. Shatsky, R. Nussinov, H.J. Wolfson, Flexible Protein Alignment and Hinge Detection, Proteins, 48(2), 242-256, (2002).
  53. N. Haspel, C-J. Tsai. H.J. Wolfson and R. Nussinov, Hierarchical protein folding pathways: A computational study of protein fragments, Proteins, 51, 203—251, (2003).
  54. H. Benyamini, K. Gunasekaran, H. Wolfson and R. Nussinov, Conservation and Amyloid Formation: A Study of the Gelsolin-Like Family, Proteins, 51, 266—282, (2003).
  55. D. Schneidman-Duhovny, Y. Inbar, V. Polak, M. Shatsky, H. Benyamini, A. Barzilay, O. Dror, N. Haspel, R. Nussinov, and H.J. Wolfson, Taking Geometry to its Edge: Fast Unbound Rigid (and Hinge-bent) Docking, Proteins, 52, 107—112, (2003).
  56. N. Haspel, C-J. Tsai, H. Wolfson, and R. Nussinov, Reducing the Computational Complexity of Protein Folding via Fragment Folding and Assembly, Protein Science 12, 1177—1187, (2003).
  57. A. Oron, K. Gunasekaran, H. Wolfson, and R. Nussinov, Using 'DelPhi' to Compute Electrostatic Potentials and Asses their Contribution to Interactions, Current Protocols in Bioinformatics, 8.4.1-8.4.12, (2003).
  58. B. Ma, T. Elkayam, H. Wolfson and R. Nussinov, Protein-protein Interactions: Structurally Conserved Residues Distinguish between Binding Sites and Exposed Protein Surfaces, Proc. Nat. Acad. Sc., USA, 100(10), 5772—5777, (2003).
  59. I. Halperin, H.J. Wolfson, and R. Nussinov, SiteLight: Binding Site Prediction using Phage Display Libraries, Protein Science, 12, 1344-1359, (2003).
  60. H. Benyamini, K. Gunasekaran, H. Wolfson & R. Nussinov, 2-Microglobulin Amyloidosis: Insight from Conservation Analysis and Fibril Modelling by Protein Docking Techniques, J. Mol. Biol. 330, 159—174, (2003).
  61. O. Dror, H. Benyamini, R. Nussinov, H.J. Wolfson, MASS : A Method for Multiple Structural Alignment by Secondary Structures, Bioinformatics, Vol. 19, suppl. 1 (ISMB’03 issue), pp. i95-i104 (2003).
  62. Y. Inbar, H. Benyamini, R. Nussinov, H.J. Wolfson, Protein Structure Prediction via Combinatorial Assembly of Sub-structural Units, Bioinformatics, Vol. 19, suppl. 1 (ISMB’03 issue), pp. i158-i168 (2003).
  63. O. Dror, H. Benyamini, R. Nussinov, H.J. Wolfson, Multiple Structural Alignment by Secondary Structures: An Algorithm and Applications, Protein Science 12, 2492-2507, (2003).
  64. M. Shatsky, R. Nussinov, H.J. Wolfson, FlexProt: Alignment of Flexible Protein Structures without a Predefinition of Hinge Regions, J. Computational Biology, 11(1), 83—106, (2004).
  65. O. Dror, A. Shulman, R. Nussinov, and H.J. Wolfson, Predicting Molecular Interactions in Silico: I. A guide to Pharmacophore Identification and its Applications to Drug Design, Curr. Med. Chem. 11(1), 71--90, (2004).
  66. D. Schneidman, R. Nussinov, and H.J. Wolfson, Predicting Molecular Interactions in Silico: II. Protein-Protein and Protein-Drug Docking, Curr. Med. Chem. 11(1), 91—107, (2004).
  67. M. Shatsky, R. Nussinov, H.J. Wolfson, A Method for Simultaneous Alignment of Multiple Protein Structures, Proteins 56, 143—156, (2004).
  68. O. Keskin, C.-J. Tsai, H. Wolfson and R. Nussinov, A New, Structurally Non-Redundant, Diverse Dataset of Protein-Protein Interfaces and its Implications, Protein Science, 13, 1043—1055, (2004).
  69. A. Barzilay, 'S. Kumar', H. Wolfson and R. Nussinov, A Potential Folding-Function Inter-relationship in Proteins, Proteins, 56, 635—649, (2004).
  70. T.Gidalevitz, C. Biswas, H. Ding, D. Schneidman-Duhovny, H.J. Wolfson, F. Stevens, S. Radford, and Y. Argon, Identification of N-terminal peptide binding site of GRP94, J. Biol. Chem., 279(16), 16543—16552, (2004).
  71. A. Shulman, R. Nussinov and H. J. Wolfson, Recognition of Functional Sites in Protein Structures, J. Mol. Biol., 339, 607—633, (2004).
  72. I. Halperin, H. Wolfson, and R. Nussinov, Protein-Protein Interactions: Coupling of Structurally Conserved Residues and of Hot Spots across Interfaces. Implications for Docking, Structure, 12, 1027—1038, (2004).
  73. M. Shatsky, O. Dror, D. Schneidman-Duhovny, R. Nussinov, H. Wolfson, BioInfo3D: A Suite of Tools for Structural Bioinformatics, Nuc. Acids Res., 32 (NAR, web server issue), W503—W507, (2004).
  74. D. Zanuy, 'N. Haspel', H.H. Tsai, B. Ma, K. Gunasekaran, H. J. Wolfson and R. Nussinov, Side chain interactions determine the amyloid organization: A single layer -sheet molecular structure of the calcitonin peptide segment 15 – 19, Phys., Biol., 1, 89—99, (2004).
  75. H. J. Wolfson, M. Shatsky, D. Duhovny, A. Shulman, B. Ma, and R. Nussinov, Structural Bioinformatics: Advanced Tools for Structural Pattern Discovery in Proteins, Current Protein & Peptide Science, 6 (2), 171—183, (2005).
  76. Y. Inbar, H. J. Wolfson, R. Nussinov, Multiple Docking for Protein Structure Prediction, Int. J. Robotics Research, 24, 131--150, (2005).
  77. N. Haspel, D. Zanuy, B. Ma, H. Wolfson, and R. Nussinov, A comparative study of amyloid fibril formation by residues 15-19 of the human calcitonin hormone: A single b-sheet model with a small hydrophobic core, J. Mol. Biol., 345(5), 1213—1227, (2005).
  78. S. Mintz, A. Shulman-Peleg, H. Wolfson and R. Nussinov, Generation and Analysis of a Protein-Protein Interface Dataset with Similar Chemical and Spatial Patterns of Interactions, Proteins, 61, 6--20, (2005).
  79. D. Schneidman-Duhovny, Y. Inbar, R. Nussinov and H. J. Wolfson, Geometry Based Flexible and Symmetric Protein Docking, Proteins, 60, 217--223, (2005).
  80. Y. Inbar, D. Schneidman-Duhovny, I. Halperin, A. Oron, R. Nussinov and H.J. Wolfson, Approaching the CAPRI Challenge with an Efficient Geometry Based Docking, Proteins, 60, 224--231, (2005).
  81. D. Schneidman-Duhovny, Y. Inbar, R. Nussinov and H. J. Wolfson, PatchDock and SymmDock: servers for rigid and symmetric docking, Nuc. Acids Res., 33 (NAR, web server issue), W363—W367, (2005).
  82. A. Shulman-Peleg, R. Nussinov and H. J. Wolfson, SiteEngines: Recognition and Comparison of Binding Sites and Protein-Protein Interfaces, Nuc. Acids Res. 33 (NAR, web server issue), W337—W341, (2005).
  83. Y. Inbar, H. Benyamini, R. Nussinov, H. J. Wolfson, Prediction of Multi-Molecular Assemblies by Multiple Docking, J. Mol. Biol., 349(2), 241—449, (2005).
  84. O. Dror, R. Nussinov, H.J. Wolfson, ARTS: Alignment of RNA Tertiary Structures, Bioinformatics, Vol. 21, (ECCB’2005 issue), ii47—ii53, (2005).
  85. H. Benyamini, K. Gunasekaran, H. Wolfson and R. Nussinov, Fibril Modeling by Sequence and Structure Conservation Analysis Combined with Protein Docking Techniques: 2-Microglobulin Amyloidosis, Biochim Biophys Acta, 1753, 121—130, (2005).
  86. Y. Inbar, H. Benyamini, R. Nussinov, and H. J. Wolfson, Combinatorial Docking Approach for Structure Prediction of Large Proteins and Multi-Molecular Assemblies, J. Phys. Biol, 2, S156—S165, (2005).
  87. M. Shatsky, R. Nussinov, H.J. Wolfson, Optimization of Multiple Sequence Alignment Based on Multiple Structure Alignment, Proteins, 62, 209—217, (2006).
  88. C. Aleman, D. Zanuy, A.I. Jimenez, C. Cativiela, N. Haspel, J. Zheng, J. Casanovas, H. Wolfson and R. Nussinov, Concepts and Schemes for the Re-engineering of Physical Protein Modules: Generating Nanodevices via targeted Replacements with Constrained Amino Acids, J. Phys. Biol, 2 (4), 156—165, (2006).
  89. M. Shatsky, A. Shulman-Peleg, R. Nussinov and H.J. Wolfson, The Multiple Common Point Set Problem and its Application to Molecule Binding Pattern Detection, J. of Computational Biology (special RECOMB’2005 issue), 13(2), 407—428, (2006).
  90. I. Halperin, H. Wolfson and R. Nussinov, Correlated Mutations: Advances and Limitations. A study on Fusion Proteins and the Cohesin-Dockerin Families, Proteins, 63(4), 832—845, (2006).
  91. H. Benyamini, A. Shulman-Peleg, H.J. Wolfson, B. Belogorodsky, L. Fadeev and M. Gozin, Interaction of C60-Fullerene and Carboxyfullerene with Proteins: Docking and Binding Site Alignment, Bioconjugate Chemistry, 17(2), 378—386, (2006).
  92. G. Weinreb, N. Haspel, H. J. Wolfson, and R. Nussinov, A permissive secondary structure-guided superimposition tool for clustering of protein fragments toward protein structure prediction via fragment assembly, Bioinformatics 22(11), 1343—1352, (2006).
  93. O. Dror, R. Nussinov, H.J. Wolfson, The ARTS web server for aligning RNA tertiary structures, Nuc. Acids Res. 34 (NAR, web server issue), W412—W415, (2006).
  94. N. Haspel, D. Zanuy, C. Aleman, H. Wolfson and R. Nussinov, De novo tubular nanostructure design based on self-assembly of beta-helical protein motifs, Structure, 14 (7), 1137—1148, (2006).
  95. O. Dror, K. Lasker, R. Nussinov and H. Wolfson, EMatch: An Efficient Method for Aligning Atomic Resolution Subunits into Intermediate Resolution cryo-EM Maps of Large Macromolecular Assemblies, Acta Cryst. Sect. D63: Biological Crystallography, 42—49, (2007).
  96. K. Lasker, O. Dror, M. Shatsky, R. Nussinov, and H. Wolfson, EMatch: Discovery of High Resolution Structural Homologues of Protein Domains in Intermediate Resolution Cryo-EM, IEEE/ACM Trans. on Computational Biology and Bioinformatics, 4(1), 28—39, (2007).
  97. C-J. Tsai, J. Zheng, D. Zanuy, N. Haspel, H. Wolfson, C. Aleman and R. Nussinov, Principles of Nanostructures Design with Protein Building Blocks, Proteins, 68(1), 1—27, (2007).
  98. D. Fishelovitch, S. Shaik, H. J. Wolfson, R. Nussinov , Structural dynamics of the cooperative binding of organic molecules in the human Cytochrome P450 (Cyp450) 3A4, J. Amer. Chem. Soc. (JACS), 129(6), 1602—1611, (2007).
  99. U. Emekli, D. Schneidman-Duhovny, H. J. Wolfson, R. Nussinov, T. Haliloglu, HingeProt: Automated Prediction of Hinges in Protein Structures, Proteins, 70(4), 1219—1227, (2007).
  100. N. Haspel, D. Zanuy, J. Zheng, C. Aleman, H. Wolfson and R. Nussinov, Changing the charge distribution of -helical based nanostructures can provide the conditions for charge transfer, Biophysical J., 93(1), 245—253, (2007).
  101. N. Andrusier, R. Nussinov, H. J. Wolfson, FireDock: Fast Interaction Refinement in Molecular Docking, Proteins, 69, 139—159, (2007).
  102. A. Shulman-Peleg, M. Shatsky, R. Nussinov and H. J. Wolfson, Spatial chemical conservation of hot spot interactions in protein-protein complexes, BMC Biology , 5:43 (11pp), (2007).
  103. N. Miled, Y. Yan, W-C. Hon, O. Perisic, M. Zvelebil, Y. Inbar, D. Schneidman-Duhovny, H. J. Wolfson, J.M. Backer and R. L. Williams, Mechanism of two classes of Cancer Mutations in the Phosphoinoisitide 3-Kinase Catalytic Subunit, Science, 317 (5835), 239—241, (2007).
  104. D. Schneidman-Duhovny, R. Nussinov and H. J. Wolfson, Automatic Prediction of Protein Interactions with Large Scale Motion, Proteins, 69 (4), 764—773, (2007).
  105. D. Fischelovitch, C. Hazan, H. Hirao. H.J. Wolfson, R. Nussinov, S. Shaik, QM/MM study of the active species of the human cytochrome P450 3A4, and the influence thereof of the multiple substrate binding, J Phys Chem B., 111(49), 13822—13832, (2007).
  106. M. K. Julsing, N. P. Vasilev, D. Schneidman-Duhovny, R. Muntendam, H. J. Woerdenbag, W. J. Quax, H. J. Wolfson, I. Ionkova, O. Kayser, Metabolic stereoselectivity of cytochrome P450 3A4 towards deoxypodophyllotoxin: in silico predictions and experimental validation, European J. of Medicinal Chemistry , 43(6):1171--1179, (2008).
  107. M. Topf, K. Lasker, B. Webb, H. Wolfson, W. Chiu. A. Sali, Protein Structure Fitting and Refinement Guided by Cryo-EM Density, Structure, 16(2), 295—307, (2008).
  108. I. Kifer, R. Nussinov, H.J. Wolfson, Constructing Templates for Protein Structure Prediction by Simulation of Protein Folding Pathways, Proteins, 73(2):271-289, (2008).
  109. E. Mashiach, D. Schneidman-Duhovny, N. Andrusier, R. Nussinov, H. J. Wolfson, FireDock: A Web Server for Fast Interaction Refinement in Molecular Docking, Nucleic Acids Research (NAR), Voll. 36, W229—232, (2008).
  110. D. Schneidman-Duhovny, O. Dror, Y. Inbar, R. Nussinov, H. J. Wolfson, PharmaGist: a Web Server for Ligand Based Pharmacophore Detection, Nucleic Acids Research. (NAR), Vol. 36, W223--228, (2008).
  111. A. Shulman-Peleg, M. Shatsky, R. Nussinov, H. J. Wolfson, MultiBind and MAPPIS: Web servers for multiple alignment of protein 3D binding sites and their interactions, Nucleic Acids Research (NAR), Vol.36, W260--W264, (2008).
  112. E. Yaffe', D. Fischelovitch, H. J. Wolfson, D. Halperin, R. Nussinov,' MolAxis: A server for Identification of Channels in Macromolecules, Nucleic Acids Research (NAR), Vol. 36, W210—215, (2008).
  113. A. Shulman-Peleg, M. Shatsky, R. Nussinov, H. J. Wolfson, Prediction of interacting single-stranded RNA bases by protein binding patterns, J. Mol. Biol, 379 (2), 299—316, (2008).
  114. E. Yaffe', D. Fischelovitch, H. J. Wolfson, D. Halperin, R. Nussinov,' MolAxis: Efficient and Accurate Identification of Channels in Macromolecules, Proteins, 73(1):72--86, (2008).
  115. N. Andrusier, E.Mashiach, R. Nussinov, H. J. Wolfson, Principles of flexible protein-protein docking, Proteins, 73(2):271-289, (2008).
  116. D. Schneidman-Duhovny, O. Dror, Y. Inbar, R. Nussinov, H. J. Wolfson, Deterministic Pharmacophore Detection via Multiple Flexible Alignment of Drug-Like Molecules, J Comput Biol., 15(7): 737-754, (2008).
  117. O. Dror, D. Schneidman-Duhovny, A. Shulman-Peleg, R. Nussinov, H. J. Wolfson and R. Sharan, Structural Similarity of Genetically Interacting Proteins, BMC Systems Biology (2008), 2:69 (7pp.); doi:10.1186/1752-0509-2-69.
  118. M. Abraham, O. Dror, R. Nussinov, H. J. Wolfson, Analysis and classification of RNA tertiary structures, RNA, 14: 2274-2289, (2008).
  119. A. Shulman-Peleg, M. Shatsky, R. Nussinov, H. J. Wolfson, RsiteDB: a database of protein binding pockets that interact with RNA nucleotide bases, Nucleic Acids Research, Vol.37, D369-|D373, (2009) ; doi: 10.1093/nar/gkn759.
  120. K. Lasker, M. Topf, A. Sali, H.J. Wolfson, Inferential optimization for fitting multiple components into a cryoEM map of their assembly, J. Mol. Biol. 388: 180-194, (2009).
  121. D. Fischelovitch, S. Shaik, H.J. Wolfson, R. Nussinov, Theoretical characterization of substrate access/exit channels in the human cytochrome P450 3A4 enzyme: involvement of phenylalanine residues in the gating mechanism, J Phys Chem B., 113(39), 13018—13025, (2009).
  122. I. Buch, B.R. Brooks, H.J. Wolfson, R. Nussinov, Computational Validation of Protein Nanotubes, Nano Lett., 9(3), 1096—1102, (2009).
  123. O. Dror, D. Schneidman-Duhovny, Y. Inbar, R. Nussinov, H.J. Wolfson, Novel approach for efficient pharmacophore-based virtual screening: method and applications, J Chem Inf Model., 49(10), 2333-2343, (2009).
  124. E. Mashiach, R. Nussinov, H.J. Wolfson, FiberDock: Flexible Induced-fit Backbone Refinement in Molecular Docking, Proteins, 78(6), 1503—1519, (2010).
  125. D. Fischelovitch, S. Shaik, H.J. Wolfson, R. Nussinov, How does the reductase help to regulate the catalytic cycle of cytochrome P450 3A4 using the conserved water channel?, J Phys Chem B., 114(17), 5964—5970, (2010).
  126. E. Mashiach', R. Nussinov, H.J. Wolfson,' FiberDock: A Web Server for Flexible Induced-Fit Backbone Refinement in Molecular Docking, Nucl. Acids Res. 38(suppl 2), W457-W461, (2010), doi:10.1093/nar/gkq373.
  127. E. Mashiach, D. Schneidman-Duhovny, A. Peri, Y. Shavit, R. Nussinov, H.J. Wolfson, An Integrated Suite of Fast Docking Algorithms, Proteins, 78(15), 3197—3204, (2010).
  128. K. Lasker, A. Sali, H.J. Wolfson, Determining macromolecular assembly structures by molecular docking and fitting into an electron density map, Proteins, 78(15), 3205--3211, (2010).
  129. I. Buch, D. Fischelovitch, N. London, B. Raveh, H. Wolfson, R. Nussinov, Allosteric Regulation of Glycogen Synthase Kinase-3: A Theoretical Study, Biochemistry, 49(51), 1890—1901, (2010).
  130. I. Buch, C.J. Tsai, H.J. Wolfson, R. Nussinov, Symmetry-based self-assembled nanotubes constructed using native protein structures: the key role of flexible linkers, Protein Pept Lett, 18(4), 362--372 (2011).
  131. I. Kifer, R. Nussinov, H.J. Wolfson, Protein Structure Prediction using a Docking-based Hierarchical Folding Scheme, Proteins, 79(6) 1759—1773, (2011).
  132. I. Kifer, R. Nussinov, H.J. Wolfson, GOSSIP: A Method for Fast and Accurate Global Alignment of Protein Structures, Bioinformatics, 27(7), 925—932, (2011).
  133. E. Mashiach-Farkash, R. Nussinov, H.J. Wolfson, SymmRef: A Flexible Refinement Method for Symmetric Multimers, Proteins, in press, (2011), doi:10.1002/prot.23082
  134. E. Tjioe, K. Lasker, B. Webb, A. Sali, H.J. Wolfson, Multifit: a web server for fitting multiple protein structures into their electron microscopy density map, Nucl. Acids Res., in press, (2011).
  135. I. Banitt, H.J. Wolfson, ParaDocka Flexible DNA rigid protein geometric complementarity based docking algorithm, submitted.
  136. F. Karchemsky, E. Drug, E. Mashiach-Farkash, H. Wolfson, M. Gozin, O. Regev, Milk – a Surprising Diameter-Sensitive Dispersant for Carbon Nanotubes, submitted.

Chapters in Books

  1. G. Burdea, H.J. Wolfson, Solving Jigsaw Puzzles Using a Robot, In "Intelligent Robotic Systems" (S. Tzafestas, ed.), Marcel Dekker Inc., New York, Chapter 17, 637-671 (1991).
  2. Y. Yeshurun, D. Reisfeld, H. Wolfson, Symmetry: a Context Free Cue for Foveated Vision, In ``Neural Networks for Perception" (H. Wechsler, ed.), Academic Press, Vol. 1, Chapter II.15, 477-491, (1992).
  3. H.J. Wolfson, Y. Lamdan, Transformation Invariant Indexing, In ``Geometric Invariants in Computer Vision" (J. Mundy, A. Zisserman, eds.), MIT Press, Chapter 17, 335-353 (1992).
  4. H.J. Wolfson and R. Nussinov, From Computer Vision to Protein Structure and Association, In ``Computational Methods in Molecular Biology” (S. Salzberg, D.B. Searls, S. Kasif, eds.), Elsevier Science B.V., Chapter 14, 313-334 (1998).
  5. H.J. Wolfson, R. Nussinov, Geometrical Docking Algorithms: A Practical Approach, In ``Methods in Molecular Biology, vol. 143 : Protein Structure Prediction", (D. Webster, ed.), Humana Press, Totowa, NJ, Chapter 17, 377-397, (2000).
  6. C. J. Tsai, R. Norel, H. Wolfson, J. V. Maizel, and R. Nussinov, Protein-ligand interactions: Energetic contributions and shape complementarity, In ``Encyclopedia of Life Sciences" (S. Robertson, ed.), London, Macmillan Publishers Ltd., Nature Publishing group, 8pp., web-based encyclopedia www.els.net, (2001) .
  7. B. Ma, S. Kumar, C. J. Tsai, H.J. Wolfson, N. Sinha, and R. Nussinov, Protein-ligand interactions: Induced Fit? , In ``Encyclopedia of Life Sciences" (S. Robertson, ed.), London, Macmillan Publishers Ltd., Nature Publishing group, 8pp., web-based encyclopedia www.els.net, (2001) .
  8. R. Nussinov, B. Ma, and H.J. Wolfson , Computational Methods for Docking and Applications to Drug Design: Functional Epitopes and Combinatorial Libraries, In "Current Topics in Computational Biology" (T. Jiang, Y. Xu, M.Q. Zhang, ed.’s), MIT Press, Chapter 19, 503-524, (2002).
  9. N. Haspel. C-J. Tsai, H.J. Wolfson and R. Nussinov, From the Building Blocks Model to Protein Structure Prediction, In "Protein Structure Prediction : Bioinformatic Approach" (I.Tsigelny, ed.), International University Line, La Jolla, CA., chapter 8, 201-226, (2002).
  10. S. Kumar, A. Barzilai, N. Haspel. Y.Y. Sham, C-J. Tsai, H.J. Wolfson and R. Nussinov, Critical Building Blocks in Proteins: A Common Theme for Folding and Function, In "Recent Research Developments in Protein Folding, Stability and Design" (M.M. Gromiha and S. Selvaraj, ed.’s), Chapter 15, Research Signpost, Kerala, India, (2002).
  11. H.J. Wolfson, Spatial Pattern Detection in Structural Bioinformatics, In “Mathematical Methods for Protein Structure Analysis and Design”, (C. Guerra and S. Istrail, ed.’s), Lecture Notes in Bioinformatics 2666, Springer Verlag, Chapter 2, pp. 35-56, (2003).
  12. N. Haspel, D. Zanuy, H.H. Tsai, B. Ma, H. Wolfson, and R. Nussinov, Computational approaches and tools for establishing structural models for short amyloid-forming peptides, In “Amyloid Proteins: The Beta Pleated Sheet Conformation And Disease”, (J.D. Sipe, ed.), VCH-Wiley, Chapter 13, pp. 301—316, (2005).
  13. O. Dror , A. Shulman-Peleg , R. Nussinov , H.J. Wolfson, Predicting molecular interactions in silico: 'I.' A updated guide to pharmacophore identification and its applications to drug design,. "Frontiers in Medicinal Chemistry", Vol.3, (A.U. Rahman and A.B. Reitz, eds), Bentham Science, pp. 551—584, (2006).
  14. D. Schneidman, R. Nussinov, and H.J. Wolfson, Predicting Molecular Interactions in Silico: II. Protein-Protein and Protein-Drug Docking, "Frontiers in Medicinal Chemistry", Vol.3, (A.U. Rahman and A.B. Reitz, eds), Bentham Science, pp. 585—613, (2006).
  15. 'N. Haspel', G. Weinreb, Y. Inbar, H.H. Tsai, C.J. Tsai, H.J. Wolfson, R. Nussinov, A hierarchical protein folding scheme based on the building block folding model, [javascript:AL_get(this, 'jour', 'Methods Mol Biol.'); Methods Mol Biol.], vol. 350, 189-204, (2007).
  16. M. Shatsky, R. Nussinov, H.J. Wolfson, Algorithms for Multiple Structure Alignment and Structure Derived Multiple Sequence Alignment, [javascript:AL_get(this, 'jour', 'Methods Mol Biol.'); Methods Mol Biol.], vol. 413, 125--146, (2008).
  17. 'I. Buch, C.J. Tsai, H.J. Wolfson, R. Nussinov, Self-assembly of fused homo-oligomers to create nanotubes, In Nanostructure Design: Methods and Protocols (Gazit, E. Nussinov, R., eds.), Vol. 474, pp. 117-131. Humana Press, Totowa, NJ, (2008).

Articles in Peer-Reviewed Conference Proceedings

  1. E. Kishon, H. Wolfson, 3-D Curve Matching, Proc. of the AAAI Workshop on Spatial Reasoning and Multi-Sensor Fusion, St.Charles, Illinois, Oct. 1987, pp.250-261.
  2. H. Wolfson, On Curve Matching, Proc. of the IEEE Computer Soc. Workshop on Computer Vision, Miami-Beach, Florida, Nov.30-Dec.2 1987, pp.307-310.
  3. Y. Lamdan, J.T. Schwartz, H. Wolfson, On Recognition of 3-D Objects from 2-D Images, Proc. of the IEEE International Conference on Robotics and Automation, Philadelphia, Pa., April 1988, pp. 1407-1413.
  4. Y. Lamdan, J.T. Schwartz, H.J. Wolfson, Object Recognition by Affine Invariant Matching, Proc. of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition, Ann-Arbor, Michigan, June 1988, pp. 335-344.
  5. J. Hong, H. Wolfson, An Improved Model-Based Matching Method using Footprints, Proc. of the 9'th International Conference on Pattern Recognition, Rome, Italy, Nov. 1988, pp. 72-78.
  6. Y. Lamdan, H.J. Wolfson, Geometric Hashing: A General and Efficient Model-Based Recognition Scheme, Proc. of the Second International Conference on Computer Vision, Tampa, Florida, Dec. 1988, pp. 238-249.
  7. H.J. Wolfson, Model Based Object Recognition by `Geometric Hashing’, Proc. of the First European Conference on Computer Vision, Antibes, France, April 1990, pp. 526-536, Lecture Notes in Computer Science 427, Springer Verlag.
  8. E.Kishon, H. Wolfson, T. Hastie, 3-D Curve Matching using Splines, Proc. of the First European Conference on Computer Vision, Antibes,France, April 1990, pp. 589-591, Lecture Notes in Computer Science 427, Springer Verlag.
  9. D. Reisfeld, H. Wolfson, Y. Yeshurun, Detection of Interest Points Using Symmetry, Third International Conference on Computer Vision, pp. 62-65, Dec. 1990, Osaka, Japan.
  10. E. Sali, H. Wolfson, Texture Classification in Aerial Photographs and Satellite Data, Proc. of the 7'th Israeli Conference on AI, Computer Vision and Pattern Recognition, Dec. 1990, pp. 325-334, Elsevier, North-Holland.
  11. D. Reisfeld, H. Wolfson, Y. Yeshurun, Realization of the Intuitive Notion of Symmetry for Feature Detection, Proc. of the 7'th Israeli Conference on AI, Computer Vision and Pattern Recognition, Dec. 1990, pp. 335-344, Elsevier, North-Holland.
  12. H.J. Wolfson, On the Recognition of Articulated Objects (Generalizing the Generalized Hough Transform), Proc. of the IAPR International Workshop on Visual Form, pp. 603-612, May 1991, Capri, Italy, Plenum Press.
  13. A. Beinglass, H.J. Wolfson, Articulated Object Recognition, or: How to Generalize the Generalized Hough Transform, Proc. of the 1991 IEEE Computer Society Conference on Computer Vision and Pattern Recognition, pp. 461-466, June 1991, Maui, Hawaii.
  14. Y. Lamdan, H.J. Wolfson', On the Error Analysis of `Geometric Hashing, Proc. of the 1991 IEEE Computer Society Conference on Computer Vision and Pattern Recognition, pp. 22-27, June 1991, Maui, Hawaii; (also Courant Inst. Robotics Report 213, Oct. 1989).
  15. D. Fischer, R. Nussinov, H.J. Wolfson, 3-D Substructure Matching in Protein Molecules , 3’rd Symposium on Combinatorial Pattern Matching, April 1992, Tucson, Arizona, USA, Lecture Notes in Computer Science 644, pp. 136-150, Springer-Verlag.
  16. D. Fischer, R. Norel, R. Nussinov, H.J. Wolfson, 3-D Docking of Protein Molecules, 4'th Symposium on Combinatorial Pattern Matching, June 1993, Padova, Italy, Lecture Notes in Computer Science 684, pp. 20-34, Springer-Verlag.
  17. B. Sandak, R. Nussinov, H.J. Wolfson, 3-D Flexible Docking of Molecules,Workshop on Shape and Pattern Matching in Computational Biology (held in conjunction with the 1994 IEEE Computer Society Conference on Computer Vision and Pattern Recognition), June 1994, Seattle, Washington, pp. 41-54.
  18. E. Cohen, H.J. Wolfson, Partial Matching of 3-D Objects in CAD/CAM Systems, 12’th International Conference on Pattern Recognition, Oct. 1994, Jerusalem, Israel, pp. 483-487.
  19. K. Kupeev, H.J. Wolfson, On Shape Similarity, 12'th International Conference on Pattern Recognition, Oct. 1994, Jerusalem, Israel, pp. 227-231.
  20. D. Fischer, S. Lin, R. Nussinov, H.J. Wolfson, Docking of Protein Molecules, 12'th International Conference on Pattern Recognition, Oct. 1994, Jerusalem, Israel, pp. 145-149.
  21. K.Y. Kupeev, H.J. Wolfson, Perceptual Convexity, SPIE International Symposium on Vision Geometry IV, 1995, USA, Proc. SPIE, Vol. 2573, pp.125-136 .
  22. B. Sandak, R. Nussinov, H.J. Wolfson, Docking of Conformationally Flexible Proteins, 7’th Symposium on Combinatorial Pattern Matching (CPM'96), June 1996, Laguna Beach, California, Lecture Notes in Computer Science 1075, pp. 271-287, Springer-Verlag.
  23. B. Sandak, H.J. Wolfson and R. Nussinov, Hinge-Bending at Molecular Interfaces : Automated Docking of a Dihydroxyethylene-Containing Inhibitor to the HIV-1 Protease, Biological Struct. & Dynamics, Proc. of the Ninth Conversation, State Univ. of New York, Albany, Eds. R.H. Sarma & M.H. Sarma, pp. 233-248, Adenine Press, Albany, NY, 1997.
  24. R. Norel, S.L. Lin, D. Xu, H.J. Wolfson, and R.Nussinov, Molecular Surface Variability and Induced Conformational Changes upon Protein-Protein Associations, Structure, Motion, Interaction and Expression of Biological Macromolecules, Proc. of the Tenth Conversation, State Univ. of New York, Albany, Eds. R.H. Sarma & M.H. Sarma, Vol. 2, pp. 33--51, Adenine Press, Albany, NY, 1998.
  25. N. Leibowitz, Z.Y. Fligelman, R. Nussinov, H.J. Wolfson, Multiple Structural Alignment and Core Detection by Geometric Hashing, Proc. of the 7'th International Conference on Intelligent Systems in Molecular Biology, Heidelberg, Germany, August 1999, pp. 169--177, (T. Lengauer et al., ed.’s), AAAI Press, Menlo Park, California. Received the ISMB'99 outstanding paper award.
  26. M. Shatsky, Z.Y. Fligelman, R. Nussinov, H.J. Wolfson, Alignment of Flexible Protein Structures Proc. of the 8'th International Conference on Intelligent Systems for Molecular Biology, San Diego, Ca., August 2000, pp. 329-343, (R. Altman et al.,ed.'s), AAAI Press, Menlo Park, California.
  27. M. Shatsky, R. Nussinov, H.J. Wolfson, MultiProt - a Multiple Protein Structural Alignment Algorithm, 2’nd Workshop on Algorithms in Bioinformatics (WABI’02 as part of ALGO’02), Rome, Italy, Sept. 2002, Lecture Notes in Computer Science 2452, pp. 235-250, Springer Verlag.
  28. D. Duhovny, R. Nussinov, H.J. Wolfson, Efficient Unbound Docking of Rigid Molecules, 2’nd Workshop on Algorithms in Bioinformatics (WABI’02 as part of ALGO’02), Rome, Italy, Sept. 2002, Lecture Notes in Computer Science 2452, pp. 185-200, Springer Verlag.
  29. 'A. Shulman-Peleg, S. Mintz, R. Nussinov and H. Wolfson, Protein-Protein Interfaces: Recognition of Similar Spatial and Chemical Organizations, 4’th Int. Workshop on Algorithms in Bioinformatics (WABI’04 as part of ALGO’04), Bergen, Norway, Lecture Notes in Computer Science, Vol. 3240, pp. 194--205, Springer Verlag (2004).
  30. M. Shatsky, A. Shulman-Peleg, R. Nussinov and H.J. Wolfson, Recognition of Binding Patterns Common to a Set of Protein Structures, 9’th Int. Conf. on Research in Comp. Bio. (RECOMB’2005), Boston, MA, USA, Lecture Notes in Bioinformatics, Vol. 3500, pp. 440—455, Springer Verlag (2005).
  31. K. Lasker, O. Dror, R. Nussinov, H.J. Wolfson, Discovery of protein structures in EM maps, 5’th Int. Workshop on Algorithms in Bioinformatics (WABI’05 as part of ALGO’05), Mallorca, Spain, Lecture Notes in Bioinformatics, Vol. 3692, pp. 423--434, (2005).
  32. A. Shulman-Peleg, M. Shatsky, R. Nussinov, and H.J. Wolfson, MAPPIS: Multiple 3D Alignment of Protein-Protein Interfaces, 1’st Int. Symp. on Comp. Life Sc. (CompLife’05), Konstanz, Germany, Lecture Notes in Bioinformatics, Springer Verlag , Vol. 3695, pp. 91—103, (2005).
  33. Y. Inbar, D. Schneidman-Duhovny, O. Dror, R. Nussinov and H.J. Wolfson, Deterministic Pharmacophore Detection via Multiple Flexible Alignment of Drug-Like Molecules, 11’th Int. Conf. on Research in Comp. Bio. (RECOMB'2007), Oakland USA, Apr. 2007, Lecture Notes in Computer Science, Springer, Vol. 4453, pp. 412-429, (2007).

Invited Papers in Conference Proceedings

  1. H. Wolfson, E.Schonberg, A.Kalvin, Y. Lamdan, Solving Jigsaw Puzzles by Computer, ORSA/TIMS J. Nat. Meeting, Miami Beach, Fl., Oct. 1986, p. 127 (abstract). Also 3'rd Israeli AI and Computer Vision Conf., Dec. 1986.
  2. J.T. Schwartz, H.J. Wolfson, Improved Shape-Signature and Matching Methods for Model-Based Robotic Vision, Proc. of the Workshop on Space Telerobotics, (ed. Rodriguez), Vol.II, NASA, Jet Propulsion Lab., Pasadena, California, January 1987, pp. 103-109.
  3. R. Hummel, H. Wolfson, Affine Invariant Matching, Proc. of the DARPA Image Understanding Workshop, April 1988, Cambridge, Massachusetts, pp. 351-364.
  4. H.J. Wolfson, Object Recognition by Transformation Invariant Indexing, ESPRIT Workshop on `Invariants for Recognition and Positioning' in conjunction with the 2'nd European Conf. on Computer Vision, May 1992, Genoa, Italy.
  5. H.J. Wolfson, Application of 3-D Pattern Matching to Drug Design, Proc. of the Japan-Israel Workshop on Computer Vision and Visual Communication (CVVC'94), Oct. 1994, Jerusalem, Israel, pp. 51-53.

Other Publications

  1. V.D. Milman, H. Wolfson, Topics in Finite Metric Spaces, Israel Seminar on Geometrical Aspects of Functional Analysis (1983-1984), Lecture No. IV.
  2. H. Wolfson, J.Bourgain's Proof of the Equivalence of Metric and Standard Types, Israel Seminar on Geometrical Aspects of Functional Analysis (1983-1984), Lecture No. XIII-1.
  3. I. Kirsh, H. Wolfson, A New Method for Character Recognition of Hebrew Handwriting, Eskenazy Inst. of Computer Sciences, Technical Report 241/92, Tel Aviv University, (1992(.
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