3-D Structure in Chemistry and Molecular Biology - Papers
3-D
Structure in Chemistry and Molecular Biology - Papers
List of Papers
Below, we list some papers on topics that might
be covered in the seminar. The exact list will be refined as time goes
on ...
Discrete Lattice Models
K. Dill, S. Bromberg, K. Yue, K. Fiebig, D. Yee,
P. Thomas, H.S. Chan. ``Principles of protein folding -- A perspective
from simple exact models.'' Protein Science 4(1995), 561.
W.E. Hart, S. Istrail. ``Fast protein folding
in the hydrophobic-hydrophilic model within three-eights of optimal.''
Proceedings of the ACM Symposium on Theory of Computing 1995, 157.
R. Agarwala, S. Batzoglou, V. Dancik, S. Decatur,
M. Farach, S. Hannenhalli, S. Skiena. ``Local rules for protein folding
on a triangular lattice and generalized hydrophobicity in the HP model.''
Proceedings of the ACM-SIAM Symposium on Discrete Algorithms 1997, 390.
J. T. Ngo, J. Marks, Computational complexity of a problem in
molecular-structure prediction, Protein Engineering, vol 5, no 4,
pp. 313-321, 1992.
Simplified Geometric Models of
Protein Folding
- S. Sun. P.D. Thomas, K. Dill. ``A simple protein
folding algorithm using a binary code and secondary structure constraints.''
Protein Engineering 8(1995), 769.
- K. Yue, K. Dill. ``Folding proteins with a simple
energy function and extensive conformational searching.'' Protein Science
5(1996), 254.
- K. Dill and H. S. Chan. "From Levinthal to pathways to funnels",
Nature, (4) 1 (January, 1997).
Structural Domains in Proteins
G.M. Crippen, ``The tree structural organization
of proteins.'' JMB 126(1979), 315.
G.D. Rose. ``Hierarchic organization of domains
in globular proteins.'' JMB 134(1979), 447.
L. Holm, C. Sander. ``Parser for protein folding
units.'' PSFG 19(1994), 256.
R. Srinivasan, G.D. Rose. ``LINUS: A hierarchic
procedure to predict the fold of a protein.'' PSFG 22(1995), 81.
L. Holm, C. Sander. ``Searching protein structure
databases has come of age.'' PSFG 19(1994), 165.
Distance Geometry and Molecular Conformation
G.M. Crippen, T.F. Havel, "Distance Geometry
and Molecular Conformation." Research Studies Press LTD, 1988, pp.1--23,
139--191.
B. Hendrickson, "Conditions For Unique Graph
Realizations." Siam Journal of Computing, Vol. 21, No. 1, February
1992, pp. 65--84.
B. Hendrickson, "The Molecule Problem: Exploiting
Structure in Global Optimization." Siam Journal of Computing, Vol.
5, No. 4, November 1995, pp. 835--857.
Direct Methods for the Phase Problem of x-Ray
Crystallography
G. Bricogne, "Direct Phase
Determination by Entropy Maximization and Likelihood Ranking: Status
Report and Perspectives." Acta
Cryst. (1993). D49. 37--60.
George T. DeTitta et al, "Structure Solution
by Minimal-Function Phase Refinement and Fourier Filtering. I. Theoretical
Basis." Acta Cryst. (1994). A50, 203--210.
Joseph Roenblatt and Paul D. Seymour, "The
Structure of Homometric Sets." SIAM J. Alg. Disc. Meth., Vol. 3, No.
3, September 1982.
Steven S.Skiena, Warren D.Smith, Paul Lemke,
"Reconstructing Sets From Interpoint Distances (Extended Abstract)."
1990 ACM 0-89791-362-0/90/0006/0332.
Overview Articles on Molecular Similarity
and Protein Resemblance
L. Holm, C. Sander. ``Mapping the protein universe.'' Science 273(1996),
595.
J-P. Doucet, J. Weber. ``Molecular similarity.''
in Computer-Aided Molecule Design: Theory and Applications.". Springer,
1996. pp. 328--362.
Geometric Similarity in Drug Design
G. Milne, S. Wang, M. Nicklaus. ``Molecular modeling
in the discovery of drug leads.'' JCICS 36(1996), 726.
P. Indyk, R. Motwani, S. Venkatasubramanian.
"Geometric Matching under Noise: Combinatorial Bounds and Algorithms."
P.W. Finn, L.E. Kavraki, J.C. Latombe, R. Motwani,
S. Venkatasubramanian. ``Search techniques for rational drug design.''
P.W. Finn, L.E. Kavraki, J.C. Latombe, R. Motwani,
C. Shelton, S. Venkatasubramanian, A. Yao. ``RAPID: Randomized pharmacophore
identification for drug design.'' SCG 1997, 324.
T. Akutsu, H. Tamaki, T. Tokuyama. ``Distribution
of distances and triangles in a point set and algorithms for computing
the largest common point sets." SCG 1997, 314.
T. Akutsu, M.M. Halldorsson. ``On the approxiamtion
of largest common subtrees and largest common point sets.'' Lecture Notes
in Computer Science 834, Springer, 1994, 405.
G. Milne, S. Wang, M. Nicklaus. ``Molecular modeling
in the discovery of drug leads.'' JCICS 36(1996), 726.
CS-Bio Seminar Topics
Background and Partial results on problems evolving from the Bio-CS
seminar.
Analysis of Conformational Coverage
Andrew Smellie, Scott D. Kahn, and Steven L.
Teig. "Analysis of Conformational Coverage. 1. Validation and Estimation
of Coverage." J. Chem. Inf. Comput. Sci., 1995, 35, 285-294.
Andrew Smellie, Scott D. Kahn, and Steven L.
Teig. "Analysis of Conformational Coverage. 2, Applications of
Conformational Models." J. Chem. Inf. Comput. Sci., 1995, 35,
295-304.
Lydia E. Kavraki. "Geometry and the Discovery
of New Ligands." Stanford University, Stanford, CA.
Hydrogen Bonds
J. Bernstein, R.E. Davis, L. Shimoni, N.L. Chang.
``Patterns in hydrogen bonding: Functionality and graph set analysis.''
Angewandte Chemie (International Edition in English) 34(1995), 1555.
Hans C. Andersen. "Cluster expansions for
hydrogen-bonded fluids. I. Molecular association in dilute gases."
Journal of Chemical Physics, Vol. 50, number 9, Nov. 1, 1973.
Hans C. Andersen. "Cluster expansions for
hydrogen bonded fluids. II. Dense liquids.", Journal of Chemical Physics,
Vol. 61, number 12, Dec. 15, 1974.
Hydrogen Bonds in Proteins
- I.K. McDonald, J.M. Thornton. ``Satisfying hydrogen
bonding potential in proteins.'' JMB 238(1994), 777.
- R.W.W. Hooft, C. Sander, G. Vriend. ``Positioning
hydrogen atoms by optimizing hydrogen-bond networks in protein structures.''
PSFG 26(1996), 363.
Geometric Similarity for Protein Structure
Comparison
Liisa Holm and Chris Sander. "An
Evolutionary Treasure: Unification of a Broad Set of Amidohydrolases Related
to Urease." PROTEINS: Structure, Function, and Genetics 28:72-82,
Wiley-Liss, Inc., 1997.
Gerrit Vriend and Chris Sander,
"Detection of Common Three-Dimensional Substructures in Proteins."
PROTEINS: Structure, Function, and Genetics 11:52-58 (1991).
Christine A. Orengo, Nigel P. Brown,
and William R. Taylor, "Fast Structure Alignment for Protein Databank
Searching." PROTEINS: Structure, Function, and Genetics 14:139-167
(1992).
Helen M. Grindley, Peter J. Artymiuk,
David W. Rice, and Peter Willett, "Identification of Tertiary Structure
Resemblance in Proteins Using a Maximal Common Subgraph Isomorphism Algorithm."
J. Mol. Biol. (1993) 229, 707-721.
Liisa Holm and Chris Sander, "Protein
Structure Comparison by Alignment of Distance Matrices." J. Mol. Biol.
(1993) 233, 123-138.
CS-Bio Seminar Topics
Geometric Hashing
Daniel Fischer, Raquel Norel, Ruth Nussinov, Haim
J. Wolfson. "3-D Docking of Protein Molecules."
Daniel Fischer, Ruth Nussinov, Haim J. Wolfson.
"3-D Substructure Matching in Protein
Molecules."
Haim J. Wolfson. "Model-Based Object Recognition
by Geometric Hashing."
Bilha Sandak, Ruth Nussinov, Haim J. Wolfson: Docking of
Conformationally Flexible Proteins. CPM 1996: 271-287
Daniel Fischer, Raquel Norel, Ruth Nussinov, Haim J. Wolfson: 3-D
Docking of Protein Molecules. CPM 1993: 20-34
Daniel Fischer, Ruth Nussinov, Haim J. Wolfson: 3-D
Substructure Matching in Protein Molecules. CPM 1992:
136-150
Yehezkel Lamdan, Haim J. Wolfson. "Geometric
Hashing: A General and Efficient Model-Based Recognition Scheme."
Proceedings of the Second International Conference on Computer Vision,
Tampa, FL, December 5-8, 1988.
Bilha Sandak, Ruth Nussinov and Haim J. Wolfson.
"Docking of Conformationally Flexible Proteins." Lecture Notes
in Computer Science, Combinatorial Pattern Matching, 7th Annual Symposium,
CPM 96, Laguna Beach, CA, June 1996.
Daniel Fischer, Shuo Liang Lin, Haim
J. Wolfson and Ruth Nussinov. "A Geometry-based Suite of
Molecular Docking Processes." JMB (1995) 248,
459-477.
Raquel Norel, Shuo L. Lin, Haim
J. Wolfson, and Ruth Nussinov. "Shape Complementarity at Protein-Protein
Interfaces." Biopolymers, Vol. 34, 933-940 (1994).
Other Papers