A method for optimal design of a threading scoring function

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A method for optimal design of a threading scoring function

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Annual Conference on Research in Computational Molecular Biology archive
Proceedings of the third annual international conference on Computational molecular biology table of contents

Lyon, France

Pages: 25 - 32

Year of Publication: 1999

ISBN:1-58113-069-4

Authors

Jadwiga R. Bieńkowska	BioMolecular Engineering Research Center, College of Engineering, Boston University, 36 Cummington Street, Boston, MA
Robert G. Rogers, Jr.	BioMolecular Engineering Research Center, College of Engineering, Boston University, 36 Cummington Street, Boston, MA
Temple F. Smith	BioMolecular Engineering Research Center, College of Engineering, Boston University, 36 Cummington Street, Boston, MA

Sponsors

INRIA : Institut Natl de Recherche en Info et en Automatique
SIGACT: ACM Special Interest Group on Algorithms and Computation Theory

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ACM New York, NY, USA

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REFERENCES

Note: OCR errors may be found in this Reference List extracted from the full text article. ACM has opted to expose the complete List rather than only correct and linked references.

	1	R. H. Lathrop, R. G. Rogers Jr., , T. F. Smith, and J. V. White. A bayes-optimal sequence-structure theory that unifies protein sequence-structure recognition and alignment. Bulletin o/Mathematical Biology., 60:1-33, 1998.
	2	J. Richardson. The anatomy and taxonomy of protein structures. Advan. Protein Chem., 34:167-339, 1981.
	3	A. Murzin, S. E. Brenner, T. Hubbard, and C. Chothia. SCOP: a structural classification of proteins database for the investigation of the sequences and structures. J. Mol Biol., 247:536-540, 1995.
	4	C.A. Orengo, A.D. Michie, S Jones, D.T. Jones, M.B. Swindells, and J.M. Thornton. C ATH - a hierarchic classification of protein domain structures. Structure, 5:1093-1108, 1997.
	5	R Sowdhamini, D. F. Burke, J. Huang, Kenji Mizuguchi, H. A. Nagarajaram, N Srinivasan, R. E. Steward, and T. L. Blundell. Campass: a database of structurally aligned protein superfamilies. Structure, 6:1079-1085, 1998.
	6	L. Holm and C. Sander. Dali/FSSP classification of three-dimensional protein folds. Nucleic Acids Research, 25:231-234, 1997.
	7	R. H. Lathrop and T. F. Smith. Global optimum protein threading with gapped alignment and empirical pair score functions. J. Mol. Biol., 255:641-665, 1996.
	8	D. Fisher and D. Eisenberg. Protein fold recognition using sequence-derived predictions. Protein ~qcience, 5:947-955, 1996.
	9	L. Jaxoszewski, L. Rychlewski, B. Zhang, and A. Godzik. Fold prediction by a hierarchy of sequence, threading and modeling methods. Protein Sczence, 6:676-688, 1997.
	10	M. Levitt. Competitive assessment of protein fold recognition and alignment accuracy. Proteins: Structure, Function and Genetics, Suppl. 1:92-104, 1997.
	11	A. Marchler-Bauer, M. Levitt, and S. H. Bryant. A retrospective analysis of casp2 threading. Proteins: Structure, Function and Genetics, Suppl. 1:83-91, 1997.
	12	B. Rost, R. Schneider, and C. Sander. Protein fold recognition by prediction-based threading. J. Mol. Biol., 270:471-480, 1997.
	13	R.B. Russell, R.R. Copley, and G.J. Barton. Protein fold recognition by mapping predicted secondary structures. J. Mol. Biol., 259:349-365, 1996.
	14	J.U Bowie, R. Luthy, and D. Eisenberg. A method to identify protein sequences that fold into a known threedimensional structure. Science, 253:164-170, 1991.
	15	D. Jones, W. Taylor, and J. Thornton. A new approach to protein fold recognition. Nature, 358:86-89, 1992.
	16	S. H. Bryant and C. E. Lawrence. An empiricM energy function for threading protein sequence through the folding motif. Proteins: Structure, Function and Genetics, 16:92-112, 1993.
	17	S. Miyazawa and R. L.. Jernigan. Estimation of effective interresidue contact energies from protein crystal structures:quasi-chemical approximation. Macro. molecules, 18:534-552, 1985.
	18	A. Godzik, J. Skolnick, and A. Kolinski. A topology fingerprint approach to the inverse folding problem. J. Mol. Biol., 227:227-238, 1992.
	19	M. J. Sippl. Knowledge-based potentials for proteins. Current Opinion in Structural Biology, 5:229-235, 1995.
	20	R. L. Jernigan and I. Bahar. Structure-derived potentials and protein simulations. Current Opinion in Structural Biology, 6:195-209, 1996.
	21	S. Miyazawa and R. L. Jernigan. Residue-residue potentials with a favorable contact pair term and unfavorable high packing density term, for simulation and threading, j. Mol. Biol., 256:623-644, 1996.
	22	W.R. Taylor. Multiple sequence threading: An analysis of alignment quality and stability. J. Mol. Biol., 269:902-943, 1997.
	23	J. Skolnick, L. Jaroszewski, A. Kolinski, and A. Godzik. Derivation and testing of pair potentials for protein folding, when is the quasichemical approximation correct? Protein Science, 6:676-688, 1997.
	24	D. Eisenberg and A. D. MacLachlan. Solvation energy in protein folding and binding. Nature, 319:199-203, 1986.
	25	L.A. Mirny and E.I. Shakhnovich. How to derive a protein folding potential? a new approach to an old problem. J. Mol. Biol., 264:1164-1179, 1996.
	26	V.N. Maiorov and G.M. Crippen. Contact potential that recognizes the correct folding of globular proteins. J. Mol. Biol., 227:876-888, 1992.
	27	D. T. Jones and J. M. Thornton. Potential energy functions for threading. Current Opinion in Structural Biology, 6:210-216, 1996.
	28	L. Zhang and J. Skolnick. How do potentials derived from structural databases relate to "true" potentials? Protein Science, 7:112-122, 1998.
	29	J. V. White, I Muchnik, and T. F. Smith. Modeling protein cores with Markov random fields. Mathematical Biosciences, 124:149-179, 1994.
	30	R. H. Lathrop, R. G. Rogers Jr., J.R. Biefikowska, B. K. M. Bryant, L. J. Buturovid, R. Gaitatzes, C. Nambudripad, J. V. White, and T. F. Smith. Analysis and Algorithms for Protein Sequence-Structure Alignment., page in press. S. Salzberg, D. Searls and S. Kasif, Elsevier Press, Amsterdam, Netherlands, 1998.
	31	L. Lo Conte and T. F. Smith. Visible volume: A robust measure for protein structure characterization. J. Mol. Biol., 273(1):338-348, 1997.
	32	Temple F. Smith , Loredana Lo Conte , Jadwiga Bienkowska , Bob Rogers , Chrysanthe Gaitatzes , Richard Lathrop, The threading approach to the inverse protein folding problem, Proceedings of the first annual international conference on Computational molecular biology, p.287-292, January 20-23, 1997, Santa Fe, New Mexico, United States [doi>10.1145/267521.267887]
	33	C. M Stultz, R. Nambudripad, R. H. Lathrop, and J. V. White. Predicting protein stucture with probabilistic models. In N Allewell and C. Woodward, editors, Protein Folding and Stability, Greenwich, England, 1995. JAI Press.
	34	L. Holm and C. Sander. Touring protein fold space with Dali/FSSP. Nucleic Acids Research, 26:316-319, 1998.
	35	A. Marchler-Bauer and S. H. Bryant. Measures of threading specificity and accuracy. Proteins: Structure, Function and Genetics, Suppl. 1:74-82, 1997.
	36	S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman. Basic local alignment search tool. J. Mol. Biol., 215:403-410, 1990.
	37	J. R. Biefikowska, R. G. Rogers jr., and T. F. Smith. Filtered contacts threading, in preparation, 1998.
	38	F. C. Bernstein, T. F. Koetzle, G. J. B. Williams, E. F. Meyer, M. D. Brice, J. R. Rodgers, O. Kennard, T. Shimanouchi, and M. Tasumi. The protein data bank: a computer-based archival file for macromolecular structures. J. Mol. Biol., 112:535-542, 1977. Brookhaven Protein Data Bank release 80.
	39	S. E. Brenner, C. Chothia, and T. Hubbard. Population statistics of protein structures: lessons from structural classifications. Current Opinion in Structural Biology, 7:369-376, 1997. The best quality fold representatives were obtained thanks to the courtesy of S. Brenner.
	40	W. Kabsch and C. Sander. Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopoly. reefs, 22:2577-2637, 1983.