July,
2008

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, 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.
Benyaminy, 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, b2-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 b-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.
Benyaminy, K. Gunasekaran, H. Wolfson and R. Nussinov, Fibril Modeling by Sequence
and Structure Conservation Analysis Combined with Protein Docking Techniques: b2-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 b-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.
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 , in press, (2007).

106.
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).

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, (2008), (Epub ahead of
print – April 23), in press.

109.
E. Mashiach, D. Schneidman-Duhovny, N. Andrusier, R. Nussinov, H. J. Wolfson, FireDock:
A Web Server for Fast Interaction Refinement in Molecular Docking,  Nuc. Acids Res. (NAR, web server issue), W229—232,
(2008).

110.
D. Schneidman-Duhovny, O. Dror, Y. Inbar,  R. Nussinov, H. J. Wolfson, A
Web Server for Ligand Based Pharmacophore Detection, Nuc. Acids Res. (NAR, web server
issue), 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,  Nuc. Acids Res. (NAR, web server issue),       W260—264, (2008).

112.
E. Yaffe, D. Fischelovitch, H. J. Wolfson, D. Halperin, R. Nussinov, MolAxis: A server for Identification of Channels
in Macromolecules, Nuc. Acids Res. (NAR, web server issue), 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, (2008), (Epub ahead of
print – April 07), in press.

115.
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), accepted.

CHAPTERS IN BOOKS

116.
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).

117.
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).

118.
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).

119.
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).

120.
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).

121.
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) .

122.
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) .

123.
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).

124.
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).

125.
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).

126.      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).

127.      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).

128.      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).

129.      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).

130.      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, Methods Mol
Biol., vol. 350, 189-204, (2007).

131.      M. Shatsky,
R. Nussinov, H.J. Wolfson, Algorithms for Multiple Structure Alignment and Structure Derived Multiple Sequence Alignment, Methods Mol
Biol., vol. 413, 125--146, (2007).

ARTICLES IN PEER-REVIEWED
CONFERENCE PROCEEDINGS

132.
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.

133.
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.

134.
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.

135.
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.

136.
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.

137.
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.

138.
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.

139.
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.

140.
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.

141.
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.

142.
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.

143.
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.

144.
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.

145.
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).

146.
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.

147.
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.

148.
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.

149.
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.

150.
K. Kupeev, H.J. Wolfson, On Shape Similarity, 12'th
International Conference on Pattern Recognition, Oct. 1994, Jerusalem, Israel, pp. 227-231.

151.
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.

152.
K.Y.  Kupeev,
H.J. Wolfson,
Perceptual Convexity, SPIE International Symposium
on Vision Geometry IV, 1995, USA, Proc. SPIE, Vol. 2573, pp.125-136 .

153.
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.

154.
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.

155.
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.

156.
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.

157.
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.

158.
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.

159.
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.

160.
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).

161.
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).

162.
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).

163.
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).

164.
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

165.
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.

166.
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.

167.
R. Hummel, H. Wolfson, Affine Invariant Matching, Proc. of the DARPA Image
Understanding Workshop, April 1988, Cambridge, Massachusetts, pp. 351-364.

168.
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.

169.
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

170.
V.D. Milman, H. Wolfson, Topics in Finite Metric
Spaces, Israel Seminar on Geometrical Aspects
of Functional Analysis (1983-1984), Lecture No. IV.

171.
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.

172.
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(.