References

Basics

L. Stryer. Biochemistry. W.H. Freeman and Co., NY, 1995. [Chapter 2]

J.J. Craig. Introduction to Robotics: Mechanics and Control. 2nd edition, Addison-Wesley, Boston, 1989. [Chapters 2 through 5]

P. Koehl. The Bio eBook. Volume, Surface, and Pockets of Proteins. http://biosimulation.stanford.edu/koehl/BioEbook/protsurf.php

M. Zhang and L.E. Kavraki. A New Method for Fast and Accurate Derivation of Molecular Conformations. J. of Chemical Information and Computing Sciences, 42:64-70, 2002.
 

Sequence similarity

C. Notredame, D. G. Higgins and J. Heringa.  T-Coffee: A Novel Method for Fast and Accurate Multiple Sequence Alignment. J. Mol Biol (2000) 302, 205-217

J. D. Thompson, D. G. Higgins and T. J. Gibson. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research, 1994, Vol. 22, No. 22, 4673-4680

R. C. Edgar. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research, 2004, Vol. 32, No. 5, 1792-1797

A. L. Simon, E. A. Stone, and A. Sidow. Inference of functional regions in proteins by quantification of evolutionary constraints. Proc. Nat. Acad. Sci., 2002, vol. 99, no. 5, 2912–2917

 

Sequence motif identification

S. F. Altschul, T. L. Madden, A. A. Schäffer, J. Zhang, Z. Zhang, W. Miller and D. J. Lipman. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research, 1997, Vol. 25, No. 17, 3389–3402

B. Berger, D. B. Wilson, E. Wolf, T. Tonchev, M. Milla and P. S. Kim. Predicting coiled coils by use of pairwise residue correlations. Proc. Nat. Acad. Sci, 1995, Vol 92, 8259-8263.

L. Cowen, P. Bradley, M. Menke, J. King and B. Berger. Predicting the Beta-Helix Fold from Protein Sequence Data. J. Comput. Biol. 9(2), 2002, 261-276.

D. T. Jones. Protein Secondary Structure Prediction Based on Position-specific Scoring Matrices. J. Mol. Biol. (1999) 292, 195-202.

 

Structure similarity

Michael A. Erdmann. Protein Similarity from Knot Theory: Geometric Convolution and Line Weavings. CMU-CS-04-138. Computer Science, Carnegie Mellon. May 16, 2004.

A.P. Singh and D.L. Brutlag. Hierarchical Protein Structure Superposition Using Both Secondary and Atomic Representations. Proc. ISMB, pp. 284-293, 1997.

J. Shapiro and D.L. Brutlag. FoldMiner: Structural Motif Discovery Using an Improved Superposition Algorithm. Protein Science, 13:278-294, 2004.

P.W. Finn, L.E. Kavraki, J.C. Latombe, R. Motwani, C. Shelton, S. Venkatasubramanian, and A. Yao. RAPID: Randomized Pharmacophore Identification for Drug Design. Computational Geometry: Theory and Applications, 10, pp. 263-272, 1998.

Protein Data Bank (PDB): http://www.rcsb.org/pdb/

Protein classification:
    SCOP: http://scop.berkeley.edu/
    CATH http://www.biochem.ucl.ac.uk/bsm/cath/

Protein alignment:
    DALI: http://www.ebi.ac.uk/dali/
    LOCK: http://dlb3.stanford.edu/LOCK/

 

Shape matching

P. H. Schonemann. A generalized solution of the orthogonal procrustes problem.  Psychometrika, 31, 1-10, 1966.

Horn, B.K.P., Closed-Form Solution of Absolute Orientation using Unit Quaternions, Journal of the Optical Society A, Vol. 4, No. 4, pp. 629–642, April 1987.

S. Umeyama, Least squares estimation of transformation parameters between two point sets, IEEE
Trans. Pattern Anal. Mach. Intell. 13 (4) (1991) 376–380.

P. J. Besl and N. D. McKay. A method for registration of 3-d shapes. IEEE Trans. Pat. Anal. and Mach. Intel. 14(2), pp 239-256, Feb 1992.

H. Pottman and M. Hofer. Geometry of the squared distance function to curves and surfaces. Vienna Institute of Technology Technical Report No.90, January 2002.

Wolfson, H.J. and Rigoutsos, I. Geometric hashing: an overview. IEEE Computational Science and Engineering, Volume: 4 , Issue: 4 , Oct.-Dec. 1997 Pages:10 - 21

Barequet, G. and Sharir, M. Partial surface and volume matching in three dimensions. Pattern Analysis and Machine Intelligence, IEEE Transactions on ,Volume: 19 , Issue: 9 , Sept. 1997 Pages: 929 - 948

X. Pennec and N. Ayache. A geometric algorithm to find small but highly similar 3D substructures in proteins. Bioinformatics, 14(6):516--522, 1998.

H. Alt and L.J. Guibas. Discrete Geometric Shapes: Matching, Interpolation, and Approximation. In J.-R. Sack, J. Urrutia, editors, Handbook of Computational Geometry, pages 121 - 153. Elsevier Science Publishers B.V. North-Holland, Amsterdam, 1999

H. Alt and M. Godau. Computing the Fréchet distance between two polygonal curves. Internat. J. Comput. Geom. Appl., 5:75-91, 1995.

D. HuttenLocher, G. Klanderman and W. Rucklidge. Comparing Images Using the Hausdorff Distance, IEEE Trans. on Pattern Analysis and Machine Intelligence, vol. 15, no. 9, pp. 850-863, 1993 (with ).

Y. Rubner, C. Tomasi and L. J. Guibas. The Earth Mover's Distance as a Metric for Image Retrieval. International Journal of Computer Vision, 40(2) November 2000, pages 99--121

M. A. Erdmann. Protein Similarity from Knot Theory and Geometric Convolution. CMU-CS-03-181. September 2003

 

Energy models and computation

D. Halperin and M. Overmars. Spheres, Molecules, and Hidden Surface Removal. Comp. Geometry: Theory and Applications, 11(2):83-102, 1996

S. Gottschalk, M. Lin, and D. Manocha. OBB-Tree: A Hierarchical Structure for Rapid Interference Detection, Proc. ACM  SIGGRAPH, 1996.

I. Lotan, D. Halperin, F. Schwarzer and J.C. Latombe. Algorithm and Data Structures for Efficient Energy maintenance During Monte Carlo Simulation of Proteins, J. Comput. Biol., 2004.

 

Shape analysis

J. Gao, L. J. Guibas, A. Nguyen, Deformable Spanners and Applications, to appear in SoCG 2004.

H. Edelsbrunner, M. A. Facello and J. Liang. On the definition and the construction of pockets in macromolecules. Discrete Appl. Math. 88 (1998), 83-102.

H. Edelsbrunner and E. P. Mucke. Three-dimensional alpha shapes. ACM Trans. Graphics 13 (1994), 43-72.

J. Liang, H. Edelsbrunner, P. Fu, P. V. Sudharkar and S. Subramaniam. Analytic shape computation of macromolecules I: molecular area and volume through alpha shape. Proteins: Structure, Function, and Genetics 33 (1998), 
1-17.

H. Edelsbrunner. The union of balls and its dual shape. Discrete Comput. Geom. 13 (1995), 415-440.

H. Edelsbrunner. Geometry and Topology for Mesh Generation. Cambridge Univ. Press, England, 2001

 

Structure determination

G. Rhodes, Crystallography Made Crystal Clear, Academic Press; 2nd edition.

K. Wüthrich, NMR of Proteins and Nucleic Acids,  Wiley-Interscience; (September 1986).

 

Protein threading

A. G. Murzin, S. E. Brenner, T. Hubbard and C. Chothia. SCOP: A Structural Classification of Proteins Database
for the Investigation of Sequences and Structures. J. Mol. Biol. 247 (1995) 536–540.

C. Chothia, J. Gough, C. Vogel and S. A. Teichmann. Evolution of the Protein Repertoire. Science 300 (2003) 1701-1703.

A. E. Torda. Protein Threading. Submitted to The Proteomics Handbook. Nov. 2003.

C. Chothia. One thousand families for the molecular biologist. Nature 357 (1992) 543-544

J. Xu and M. Li. Assessment of RAPTOR’s Linear Programming Approach in CAFASP3. Proteins 53 (2003)  579-584

K. T. Simons, R. Bonneau, I. Ruczinski, and D. Baker. Ab Initio Protein Structure Prediction of CASP III Targets Using ROSETTA. Proteins, Suppl. 3 (1999) 171-176.

 

Closing loops

M. A. Marti-Renom, A. C. Stuart, A. Fiser, R. Sanchez, F. Melo and A. Sali. Comparative protein structure modeling of genes and genomes. Ammu. Rev. Biophys. Biomol. Struct. 29 (2000) 291-325

R. Kolodny, P. Koehl, L. Guibas and M. Levitt. Small libraries of protein fragments model native protein structure accurately. J. Mol. Biol. 323 (2002) 297-307

A. A. Canutescu and R. L. Dunbrack Jr. Cyclic coordinate descent: A robotics algorithm for protein loop closure. Protein science 12 (2003) 963-972

J. Cortes, T, Simeon, M. Renaud-Simeon and V. Tran. Geometric algorithms for te conformational analysis of long protein loops.  J. Comput. Chem. 25 (2004) 956-967

E. A. Coutsias, C. Seok, M. P. Jacobson and K. E. Dill. A kinematic view of loop closure. J. Comput. Chem. 25 (2004) 510-528

I. Lotan, H van den Bedem, A. M. Deacon and J.-C Latombe. Computing Protein Structures from electron density maps: The missing loop problem. WAFR 2004, to appear.

 

Motifs: Conservation of Sequence, Structure and Chemistry

Sequence motifs (eMOTIFs)

C. G. Nevill-Manning, T. D. Wu and D. L. Brutlag (1998). Highly Specific Protein Sequence Motifs for Genome Analysis. Proc. Natl. Acad. Sci. USA, 95(11), 5865-5871.

J. Y. Huang  and D. L. Brutlag (2001). The eMOTIF Database. Nucleic Acids Research, 29(1), 202-204.

Probabilistic Motifs

T. D. Wu,  C. G. Nevill-Manning and D. L. Brutlag (1999). Minimal-Risk Scoring Matrices for Sequence Analysis. J. Comp. Biol., 6(2), 219-235.

T. D. Wu,  C. G. Nevill-Manning and D. L. Brutlag (2000). Fast probabilistic analysis of sequence function using scoring matrices. Bioinformatics, 16, 1-12.

Structural Motifs

S. P. Bennett, L. Lu and D. L. Brutlag (2003). 3MATRIX and 3MOTIF: A Protein Structure Visualization System for Conserved sequence Motifs. Nucleic Acids Research 31(13), 3328-3332.

J. Shapiro and D. L. Brutlag (2004). FoldMiner: Structural Motif Discovery Using an Improved Superposition Algorithm. Protein Science, 13, 278-294.

Atomic motifs (FEATURES)

M. P. Liang, D. L. Brutlag and R. B. Altman (2003). Automated construction of structural motifs for predicting functional sites on protein structures. Pacific Symposium Biocomput, 204-215.

M. P. Liang, D. R. Banatao, T. E. Klein, D. L. Brutlag and R. B. Altman (2003). WebFEATURE: An interactive web tool for identifying and visualizing functional sites on macromolecular structures. Nucleic Acids Research 31(13), 3324-3327.
 

History of molecular simulation

M. Levitt. The birth of computational structural biology, Nature Struct. Biol., 8, 392 (2001)

J. N. Onuchic et. al. Protein folding funnels: the nature of the transition state ensemble, Folding & Design, 1, 441 (1996)

V. S. Pande et. al. Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing, Biopolymers, 68, 91 (2003)

C. L. Brooks III, et. al. From folding theories to folding proteins: a review and assessment of simulation studies of protein folding and unfolding, Ann. Rev. Phys. Chem., 52, 499 (2001)

S. Hammes-Schiffer et. al. Computational studies of the mechanism for proton and hydride transfer in liver alcohol dehydrogenase, J. Am. Chem. Soc., 122, 4803 (2000)

 

Motion pathway analysis

M.S. Apaydin, D.L. Brutlag, C. Guestrin, D. Hsu, J.C. Latombe, and C. Varma. Stochastic Roadmap Simulation: An Efficient Representation and Algorithm for Analyzing Molecular Motion. J. Computational Biology, 10(3-4):257-281, 2003.

 

Molecular Dynamics

A.R. Leach. Molecular modeling: Principles and applications. Addison Wesley Longman Limited (1996): pp. 313-370.

C.L. Brooks, M. Karplus, and B. M. Pettitt. Proteins: a theoretical perspective of dynamics, structure, and thermodynamics. Advances in chemical physics, v. 71: pp 14-21.

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