New contact measures for the protein docking problem

Subscribe (Full Service)


	Search: The ACM Digital Library The Guide

	Feedback

New contact measures for the protein docking problem

Full text

Pdf (1.30 MB)

Source

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

Santa Fe, New Mexico, United States

Pages: 182 - 191

Year of Publication: 1997

ISBN:0-89791-882-7

Author

Hans-Peter Lenhof

Max-Planck-Institut für Informatik, 66123, Saarbrücken, Germany

Sponsors

SIGACT: ACM Special Interest Group on Algorithms and Computation Theory
DOE : Department of Energy

Publisher

ACM New York, NY, USA

Bibliometrics

Downloads (6 Weeks): 4, Downloads (12 Months): 12, Citation Count: 3

Additional Information:

references cited by index terms collaborative colleagues

Tools and Actions:	Request Permissions Review this Article Save this Article to a Binder Display Formats: BibTeX EndNote ACM Ref

DOI Bookmark:	Use this link to bookmark this Article: http://doi.acm.org/10.1145/267521.267547 What is a DOI?

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.

	AHP+95	t". Ackernlann, (;. {ler,'{ti;u~r~, S. posclx and (.;. Sa.gcrcr: ":~-I) Scglnet~! iermigsteclmikel, x un(l vektorwcrt. igc Bewert. ullgsfil~ktiorlen fiir syrtlbolischcs Protein- })rot.ei~-I)ockizig.", lit "Bioinfornlat. ics: {q'olll Nucleic Acids and Proteins to Cell Met. at)olism." Edite(I t)v D. S(:{tomburg alid {,. {,essel, ('BF Monograplts, vol. 18, 1()()~ 105 12,1. .... o, pp.
	BH81	W. Bennet and R. Haber: "Str~lctllral and Functiollal Aspects of l)omain Mot iol~ i~ Proteins.", (i',R,(' Crit. Rev. Biochem., vol. 15, 198,1, p. 291.
	BM92	D.J. Bacon and J. Moult: "Docking by Least- Sqtmres Fitting of Molecular Surface Patterns.", .1. Mol. Biol., vol. 225, 1992, pp. 8,19-858.
	Con1	M.L. Connolly: "Analytical Molecular Surface Calculation.'', J. Appl. Cryst., vol. 16, 1983, pp. 548--558.
	Con2	M.i,. Connolly: "Solvent Accessible Surface of Proteins and Nucleic Acid.", Science, vol. 221, 1983, pp. 709-713.
	Con3	M.L. Connolly: "Shape Complementary at the Hemoglobin al/31 Subunit Interface.", Biopolymers, vol. 25, 1986, pp. 1229-1247.
	CDJ91	J. Cherfils, S. Duquerroy and J. Janin: "Protein- Protein Recognition Analyzed by Docking Simulations.'', Proteins: Struc. Func. Genet., vol. l l, 1991, pp. 271-280.
	DSD+86	R. DesJarIais, R. Sheridan, J. Dixon, I. Kuntz and R. Venkataraghavan: "Docking Flexible Ligands to Macromolecular Receptors by Molecular Shape.", J. Med. Chem., vol. 29, 1986, pp. 2149-2153.
	DNS+92	M. Dixon, N. Nicholsen, L. Sherwchuk, W. Baase and B. Matthews: "Structure of a hinge-bending Bacteriophage T4 Lysozyme.", J. Mol. Biol. vol. 227, 1992, pp. 917-933.
	EKS+95	M. Ester, H.P. Kriegel, T. Seidl and X. Xu: "Formbasierte Suche nach komplement~iren 3D- Oberfiiichen in einer Protein-Datenbank.', in Datenbanksysteme in Biiro, Technik und Wissenschaft, G i- Fachtagung 1995, Georg Lausen (Hrsg.), Springer Verlag, pp. 373-382.
	FNN+93	Daniel Fischer , Raquel Norel , Ruth Nussinov , Haim J. Wolfson, 3-D Docking of Protein Molecules, Proceedings of the 4th Annual Symposium on Combinatorial Pattern Matching, p.20-34, June 02-04, 1993
	FLWN95	D. Fischer, S. Liang Lin, t l.L. Wolfson and R. Nussinov: "A Geometry-based Suite of Molecular Docking Processes.", J. Mol. Biol., vol. 248, 1995, pp. ,159-,177.
	FM90	H. Faber and B. Matthews: "A Mutant T4 Lysozyme Displays Five Different Crystal Conformations.'', Nature, vo{. 348, 1990, pp. 263-266.
	FVF+90	James D. Foley , Andries van Dam , Steven K. Feiner , John F. Hughes, Computer graphics: principles and practice (2nd ed.), Addison-Wesley Longman Publishing Co., Inc., Boston, MA, 1990
	GC91	M. (_;ersteirl ;til(I ('. Chot. llia: "Amtlysis of t~rotein Loop ('tosure. 'l'wo Tyl~('s of t:{itlg~,s Pr()d~lc:e ()~l~' Mot iorl iII l,actate l)(-~hvclrog(-,nase.", .}. Mol. Biol., vol. 220, 199 l, pt~. t3:/-- 1.49.
	HCT94	M. {{elnter-(-'itterich and A. ~l'ralnontano: "Pt_~Z- ZI,{:;: A New Method tbr Autoillat. ed Protein l')ockitlg Based on Surface Shape (lom{)lementarity.", ,J. Mol. Biol., vol. 235. 199,1, pp. 1021-1031.
	JK91	F. ,Iiang and S.-H. Kiln: "Soft I)o(:king: :~"latciiit~g of Molectdar Surface Cttbes.', J. Mol. Biol., vol. 219, 1991, pp. 79 .... t02.
	KSE+92	E. Katchalski-Katzir, I. Sharir, M. Eisenstein, A.A. Friesem, C. Aflalo and i.A. Vakser: "Molecular Surface Recognition: Determination of Geometric Fit between Protein and their Ligands by Correlation Techniques.'', Proc. Natl. Acad. Sci. USA, 1992, vol. 89, pp. 2195-2199.
	KBO+82	I.D. Kuntz, J.M. Blaney, S.J. Oatley, R. Langridge and T.E. Ferrin: "A Geometric Approach to Macromolecule-Ligand Interactions." J. Mol. Biol., vol. 161, 1982, pp. 269-288.
	KCF84	F.S. Kuhl, G.M. Crippen and D.K. Friesen: "A Combinatorial Algorithm for Calculating Ligand Binding.'', J. Comp. Chem., vol. 5 (1), 1984, pp. 24-34.
	Len95	H.-P. Lenhof: "An Algorithm for the Protein Docking Problem.", in "Bioinformatics: From Nucleic Acids and Proteins to Cell Metabolism." Edited by D. Schomburg and U. Lessel, GBF Monographs, vol. 18, 1995, pp. 125-139.
	Lew91	R.A. Lewis: "Clefts and Binding Sites in Protein Receptors.", in Methods in Enzymology, Editor: J.J. Langone, vol. 202, 1991, pp. 126-156.
	LK92	Andrew R. Leach , Irwin D. Kuntz, Conformational analysis of flexible ligands in macromolecular receptor sites, Journal of Computational Chemistry, v.13 n.6, p.730-748, July/Aug. 1992 [doi>10.1002/jcc.540130608]
	LNF+94	S.L. Lin, R. Nussinov, D. Fischer and H.J. Wolfson: "Molecular Surface Representations by Sparse Critical Points.", PROTEINS: Structure, Function, and Genetics, vol. 18, 1994, pp. 94-101.
	LW88	Y. Lamdan and H.J. Wolfson: "Geometric Hashins: A General and Efficient Model-Based Recognition Schelne.", In Proceedings of the IEEE Int. Conf. on Computer Vision, 1988, pp. 238-249.
	MWS96	M. Meyer, P. Wilson and D. Schomburg: "Hydrogen Bonding and Molecular Surface Shape Complementarity as a Basis for Protein Docking.", to appear in ,I. of Molecular Biology.
	MSS+89	M. Miller, J. Schneider, B. Sathyanarayana, M. Toth, G.R. Marshall, L. Clawson, L. Selk, S. Kent and A. Wlodawer: "Structure of C, omplex HIV-1 Protease with a Substrate-Based Inhibitor at. 2.3 ~ Resolution.", Science, vol. 246, 1989, pp. 11-19--1152.
	NLWN94	It. Norel, S.L. Li~, }t{.,1. Wolfson and R. Nussinov: "Shape Compementarity at. Protein-Protein Interfaces.", Biopolymers, vol. 34, 1994, pp. 9:/3--940.
	NLWN95	R. Novel. S.L. Lin. \|t.,I. Wolfson and R. Nussinov: "Molecular Surface ('.:omplementarit. y at Protein- Prot. ein Interfaces: The Crit. ical Role Played by Surface Normals at; Well Placed. Sparse, Points in Docking.", J. Mol. Biol. vol. 252. 1995, pp. 26:3-27:t.
	RSW92	J. Rini, U. Schulze-Gahnlell and 1. Wilson: "Struct. ural Evidence for Induced Fit as a Mechanism for Antigen~Ant. ibody ltecogllition.", Science, vol. 255, 199:2, pp. 959-965.
	Sun90	V. S. Sunderam, PVM: a framework for parallel distributed computing, Concurrency: Practice and Experience, v.2 n.4, p.315-339, Dec. 1990 [doi>10.1002/cpe.4330020404]
	SK91	II.K. Shoichet and I.D. Kuntz: "Protein Docking and Complementm'ity.", J. Mol. Biol., vol. 221, 1991, pp. 79-102.
	SNW95	B. Sandak, R. Nussinov and H.J. Wolfson: "An Automated Computer Vision and Robotics-based technique for 3-D Flexible Biomolecular Docking and Matching.", CABIOS, vol. 11, no. 1, 1995, pp. 87-99.
	SVC+92	A. Sali, B. Veerapandian, J.B. Cooper, D. Moss, T. Hofmann and T. Blundell: "Domain Flexibility in Aspartic Proteinases.", Proteins: Struc., Func., Genet., vol. 12, 1992, pp. 158-170.
	Wan91	Huajun Wang, Grid-search molecular accessible surface algorithm for solving the protein docking problem, Journal of Computational Chemistry, v.12 n.6, p.746-750, July 1991 [doi>10.1002/jcc.540120612]
	WWF+91	C. Weber, G. Wilder, B. yon Freyberg, R. Traber, W. Braun, H. Widmer and K. Wuthrich: "The NMR Structure of cyclosporin. A Bound to Cyclophilin in Aqueous Solution.", Biochemistry, vol. 30, 1991, pp. 656:/-6574.
	WS92	P.H. Walls and J. Sternberg: "New Algorithm to Model Protein-Protein Recognition Based on Surface Complementarity, Applications to Antibody-Antigen Docking.", j. Mol. Biol., vol. 228, pp. 227-297.

CITED BY 3

	O. Kohlbacher , A. Burchardt , A. Moll , A. Hildebrandt , P. Bayer , H.-P Lenhof, A NMR-spectra-based scoring function for protein docking, Proceedings of the fifth annual international conference on Computational biology, p.184-192, April 22-25, 2001, Montreal, Quebec, Canada
	E. Althaus , O. Kohlbacher , H.-P. Lenhof , P. Müller, A combinatorial approach to protein docking with flexible side-chains, Proceedings of the fourth annual international conference on Computational molecular biology, p.15-24, April 2000, Tokyo, Japan
	N. P. Boghossian , O. Kohlbacher , H. P. Lenhof, Rapid software prototyping in molecular modeling using the biochemical algorithms library (BALL), Journal of Experimental Algorithmics (JEA), 5, p.16-es, 2000