bicko's docking-scoring-function [37 articles] Export

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	Development of unified statistical potentials describing protein-protein interactions. [My Copy] Biophys J, Vol. 84, No. 3. (March 2003), pp. 1895-1901. by H. Lu, L. Lu, J. Skolnick posted to contact-pairing-preferences docking-scoring-function interaction-partner-prediction by bicko on 2008-09-01 18:06:03 as along with 8 people kaarsinogen mdimmic chad_davis cjeans selrac iris_2001 wilbur kgutwin
	Coevolution at protein complex interfaces can be detected by the complementarity trace with important impact for predictive docking [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 22. (3 June 2008), pp. 7708-7713. by Hocine Madaoui, RaphaÃ«l Guerois posted to co-evolution docking-scoring-function by bicko on 2008-06-12 10:37:57 as along with 8 people dfdong qluo robfsouza RebeccaHamer orr cabbagesofdoom phoenixzxl zwang
	Docking of protein molecular surfaces with evolutionary trace analysis [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 69, No. 4. (2007), pp. 832-838. by Eiji Kanamori, Yoichi Murakami, Yuko Tsuchiya, Daron M. Standley, Haruki Nakamura, Kengo Kinoshita posted to docking-scoring-function evolutionary-trace modelling-interactions by bicko on 2008-01-16 14:10:56 as along with 2 people okapi jjurban
	Combination of scoring schemes for protein docking [My Copy] BMC Bioinformatics, Vol. 8 (01 August 2007), 279. by Philipp Heuser, Dietmar Schomburg posted to docking-scoring-function by bicko on 2007-08-15 16:18:18 as along with 1 person dquest
	Integrating statistical pair potentials into protein complex prediction. [My Copy] Proteins (10 July 2007) by Julian Mintseris, Brian Pierce, Kevin Wiehe, Robert Anderson, Rong Chen, Zhiping Weng posted to contact-pairing-preferences docking-scoring-function fourier-transform by bicko on 2007-08-15 15:19:13 as along with 1 person chad_davis
	Flexible protein–protein docking [My Copy] Current Opinion in Structural Biology In Theory and simulation/Macromolecular assemblages - Joel Janin and Michael Levitt/Edward H Egelman and Andrew GW Leslie, Vol. 16, No. 2. (April 2006), pp. 194-200. by A BONVIN, posted to docking-algorithm docking-scoring-function protein-flexibility by bicko on 2007-05-18 13:50:11 as along with 12 people and 3 groups rabio timg flbarroso oteri laurabailey dgruiz aqeel yongzhao ima sangeetha gloria higueruelo Bioinformatics TSRI_MGL insilicodrug
	Physicochemical and residue conservation calculations to improve the ranking of protein-protein docking solutions [My Copy] Protein Sci, Vol. 14, No. 2. (1 February 2005), pp. 316-328. by Yuhua Duan, Boojala V. Reddy, Yiannis N. Kaznessis posted to ppi-evolution guided-docking docking-scoring-function docking-algorithm by bicko on 2007-01-15 11:08:21 as along with 3 people mkotlyar ameetsoni carlescorbi
	A fast protein-protein docking algorithm using series expansion in terms of spherical basis functions. [My Copy] Genome Inform, Vol. 16, No. 2. (2005), pp. 161-173. by K. Sumikoshi, T. Terada, S. Nakamura, K. Shimizu posted to docking-algorithm docking-scoring-function by bicko on 2007-01-08 16:40:24 as
	Residue conservation information for generating near-native structures in protein-protein docking. [My Copy] J Bioinform Comput Biol, Vol. 4, No. 4. (August 2006), pp. 793-806. by Y. Duan, B. V. Reddy, Y. N. Kaznessis posted to docking-algorithm docking-scoring-function guided-docking interface-properties by bicko on 2007-01-08 16:39:08 as
	A docking analysis of the statistical physics of protein-protein recognition. [My Copy] Phys Biol, Vol. 2, No. 1-2. (June 2005) by J. Bernauer, A. Poupon, J. Azé, J. Janin posted to docking-scoring-function interface-properties ppi-review by bicko on 2006-09-25 13:55:47 as along with 2 people drastic kintoki
	Residue frequencies and pairing preferences at protein-protein interfaces. [My Copy] Proteins, Vol. 43, No. 2. (1 May 2001), pp. 89-102. by F. Glaser, D. M. Steinberg, I. A. Vakser, N. Ben-Tal posted to contact-pairing-preferences docking-scoring-function interface-properties pairwise-substitution-matrices ppi-database by bicko on 2006-08-17 11:56:20 as along with 2 people higueruelo kgutwin
	Electrostatics in protein-protein docking. [My Copy] Protein Sci, Vol. 11, No. 3. (March 2002), pp. 571-587. by A. Heifetz, E. Katchalski-Katzir, M. Eisenstein posted to capri docking-algorithm docking-scoring-function energy-landscapes by bicko on 2006-06-23 01:35:21 as along with 1 person csrocha
	Protein docking using continuum electrostatics and geometric fit. [My Copy] Protein Eng, Vol. 14, No. 2. (February 2001), pp. 105-113. by J. G. Mandell, V. A. Roberts, M. E. Pique, et al.V. Kotlovyi, J. C. Mitchell, E. Nelson, I. Tsigelny, L. F. Ten Eyck posted to capri docking-algorithm docking-scoring-function energy-landscapes by bicko on 2006-06-23 01:24:12 as along with 2 people flbarroso tjimenez
	Modelling protein docking using shape complementarity, electrostatics and biochemical information [My Copy] Journal of Molecular Biology, Vol. 272, No. 1. (12 September 1997), pp. 106-120. by Henry A. Gabb, Richard M. Jackson, Michael J. Sternberg posted to capri docking-scoring-function fourier-transform by bicko on 2006-06-23 01:13:35 as along with 8 people and 3 groups apaydin jwm yongzhao ima ffranca cjeans selrac kintoki Radiation_Damage Stressosome TSRI_MGL
	ZDOCK: An initial-stage protein-docking algorithm [My Copy] Proteins: Structure, Function, and Genetics, Vol. 52, No. 1. (1 July 2003), pp. 80-87. by Rong Chen, Li Li, Zhiping Weng posted to capri docking-algorithm docking-benchmark docking-scoring-function fourier-transform by bicko on 2006-06-23 00:59:01 as along with 6 people and 2 groups chemrahul82 marti jwm ffranca gruppo selrac Radiation_Damage Stressosome
	GAPDOCK: a Genetic Algorithm Approach to Protein Docking in CAPRI round 1. [My Copy] Proteins, Vol. 52, No. 1. (1 July 2003), pp. 10-14. by E. J. Gardiner, P. Willett, P. J. Artymiuk posted to capri docking-algorithm docking-scoring-function by bicko on 2006-06-23 00:37:49 as
	BiGGER: a new (soft) docking algorithm for predicting protein interactions. [My Copy] Proteins, Vol. 39, No. 4. (1 June 2000), pp. 372-384. by P. N. Palma, L. Krippahl, J. E. Wampler, J. J. Moura posted to capri contact-pairing-preferences docking-algorithm docking-scoring-function by bicko on 2006-06-23 00:35:55 as along with 2 people selrac wonaya
	Scoring docking models with evolutionary information. [My Copy] Proteins, Vol. 60, No. 2. (1 August 2005), pp. 275-280. by M. Tress, D. de Juan, O. Graña, et al.M. J. Gómez, P. Gómez-Puertas, J. M. González, G. López, A. Valencia posted to docking-algorithm docking-scoring-function guided-docking interface-properties ppi-evolution by bicko on 2006-06-21 15:02:12 as along with 3 people and 2 groups marcius ameetsoni cjeans BioinfoCIPF SGU-CIPF
	Examination of shape complementarity in docking of unbound proteins. [My Copy] Proteins, Vol. 36, No. 3. (15 August 1999), pp. 307-317. by R. Norel, D. Petrey, H. J. Wolfson, R. Nussinov posted to docking-benchmark docking-scoring-function interface-properties ppi-database by bicko on 2006-05-11 14:57:42 as along with 1 person blackbart
	Atomic contact vectors in protein-protein recognition. [My Copy] Proteins, Vol. 53, No. 3. (15 November 2003), pp. 629-639. by Julian Mintseris, Zhiping Weng posted to crystal-contacts docking-scoring-function interface-properties ppi-database by bicko on 2006-03-27 16:01:45 as along with 1 person marti
	Optimal docking area: a new method for predicting protein-protein interaction sites. [My Copy] Proteins, Vol. 58, No. 1. (1 January 2005), pp. 134-143. by J. Fernandez-Recio, M. Totrov, C. Skorodumov, R. Abagyan posted to blundell-group docking-scoring-function energy-landscapes guided-docking interaction-site-prediction by bicko on 2006-02-20 14:45:16 as along with 5 people and 2 groups klexa jwm schlauchi cjeans marti Radiation_Damage Stressosome
	Free Energy Landscapes of Encounter Complexes in Protein-Protein Association [My Copy] Biophysical Journal, Vol. 76, No. 3. (March 1999), pp. 1166-1178. by C. Camacho posted to docking-scoring-function energy-landscapes interface-properties by bicko on 2006-02-20 14:38:14 as along with 4 people and 1 group whitead flbarroso ras dgront Jiang Research Group
	WHISCY: What information does surface conservation yield? Application to data-driven docking [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 63, No. 3. (15 May 2006), pp. 479-489. by Sjoerd J. de Vries, Aalt D. van Dijk, Alexandre M. Bonvin posted to docking-algorithm docking-scoring-function guided-docking interaction-site-prediction ppi-evolution by bicko on 2006-02-17 16:55:08 as along with 2 people gloria marti
	A novel method for scoring of docked protein complexes using predicted protein-protein binding sites. [My Copy] Protein Eng Des Sel, Vol. 17, No. 2. (February 2004), pp. 183-189. by K. E. Gottschalk, H. Neuvirth, G. Schreiber posted to docking-algorithm docking-scoring-function guided-docking by bicko on 2006-01-29 12:03:23 as
	Data-driven docking: HADDOCK's adventures in CAPRI. [My Copy] Proteins, Vol. 60, No. 2. (1 August 2005), pp. 232-238. by A. D. van Dijk, S. J. de Vries, C. Dominguez, H. Chen, H. X. Zhou, A. M. Bonvin posted to capri docking-algorithm docking-scoring-function guided-docking by bicko on 2006-01-26 20:35:17 as
	Data-driven docking for the study of biomolecular complexes. [My Copy] FEBS J, Vol. 272, No. 2. (January 2005), pp. 293-312. by A. D. van Dijk, R. Boelens, A. M. Bonvin posted to docking-algorithm docking-scoring-function guided-docking ppi-review by bicko on 2006-01-25 12:24:18 as along with 5 people and 1 group dgruiz anita gloria Evangelia higueruelo structure-bii
	Incorporating intermolecular distance into protein-protein docking. [My Copy] Protein Eng Des Sel, Vol. 17, No. 12. (December 2004), pp. 837-845. by H. Lei, Y. Duan posted to capri docking-algorithm docking-scoring-function by bicko on 2006-01-13 18:20:56 as
	Refinement of unbound protein docking studies using biological knowledge. [My Copy] Proteins, Vol. 61, No. 4. (1 December 2005), pp. 1059-1067. by P. Heuser, D. Baù, P. Benkert, D. Schomburg posted to docking-algorithm docking-scoring-function guided-docking hot-spots by bicko on 2006-01-13 15:28:18 as
	Combination of scoring functions improves discrimination in protein-protein docking. [My Copy] Proteins, Vol. 53, No. 4. (1 December 2003), pp. 840-854. by J. Murphy, D. W. Gatchell, J. C. Prasad, S. Vajda posted to docking-algorithm docking-scoring-function by bicko on 2006-01-12 13:27:37 as along with 3 people ras selrac kgutwin
	Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques [My Copy] Proceedings Of The National Academy Of Sciences Of The United States Of America, Vol. 89, No. 6. (15 March 1992), pp. 2195-2199. by E. Katchalski-Katzir, Shariv, M. Eisenstein, A. A. Friesem, C. Aflalo, I. A. Vakser posted to docking-scoring-function fourier-transform by bicko on 2006-01-12 12:21:19 as along with 1 person selrac
	Use of pair potentials across protein interfaces in screening predicted docked complexes. [My Copy] Proteins, Vol. 35, No. 3. (15 May 1999), pp. 364-373. by G. Moont, H. A. Gabb, M. J. Sternberg posted to contact-pairing-preferences docking-algorithm docking-scoring-function by bicko on 2005-12-06 11:56:06 as along with 4 people and 2 groups qluo jwm chaleil selrac Radiation_Damage Stressosome
	A soft, mean-field potential derived from crystal contacts for predicting protein-protein interactions. [My Copy] J Mol Biol, Vol. 283, No. 5. (13 November 1998), pp. 1037-1047. by C. H. Robert, J. Janin posted to crystal-contacts docking-scoring-function interface-properties by bicko on 2005-11-07 15:08:06 as
	Guided docking: first step to locate potential binding sites. [My Copy] Proteins, Vol. 52, No. 1. (1 July 2003), pp. 28-32. by P. W. Fitzjohn, P. A. Bates posted to docking-algorithm docking-scoring-function guided-docking interaction-site-prediction by bicko on 2005-10-21 10:47:16 as
	The Relationship between the Flexibility of Proteins and their Conformational States on Forming Protein-Protein Complexes with an Application to Protein-Protein Docking [My Copy] Journal of Molecular Biology, Vol. 347, No. 5. (15 April 2005), pp. 1077-1101. by Graham R. Smith, Michael Sternberg, Paul A. Bates posted to conformational-change docking-scoring-function interface-properties molecular-dynamics protein-flexibility by bicko on 2005-10-17 15:58:13 as along with 6 people and 3 groups ana barry aqeel yongzhao ttjoseph jteyra structural_bioinformatics Bioinformatics TSRI_MGL
	Principles of docking: An overview of search algorithms and a guide to scoring functions. [My Copy] Proteins, Vol. 47, No. 4. (1 June 2002), pp. 409-443. by Inbal Halperin, Buyong Ma, Haim Wolfson, Ruth Nussinov posted to docking-algorithm docking-scoring-function ppi-review by bicko on 2005-10-14 12:33:54 as along with 25 people and 4 groups rabio ucbcjbm flbarroso csrocha oteri timg dgruiz cantupaz apaydin chad_davis yongzhao ttjoseph nickolay ima sangeetha dgront blackbart gane5h mmuecke kazemi bpagano massivemayhem cjeans Evangelia nigham Structural Biology Group TorVergata Bioinformatics TSRI_MGL insilicodrug
	HADDOCK: A Protein−Protein Docking Approach Based on Biochemical or Biophysical Information [My Copy] Journal of the American Chemical Society, Vol. 125, No. 7. (1 February 2003), pp. 1731-1737. by Cyril Dominguez, Rolf Boelens, Alexandre M. J. J. Bonvin posted to docking-algorithm docking-scoring-function guided-docking by bicko on 2005-10-13 10:39:55 as along with 10 people bmduggan chad_davis laurabailey A_Coletta_Thesis betainverse dgruiz bluvsh1 gloria ruvido yalexeev
	Identification of Protein-Protein Interaction Sites from Docking Energy Landscapes [My Copy] Journal of Molecular Biology, Vol. 335, No. 3. (16 January 2004), pp. 843-865. by Juan Fernandez-Recio, Maxim Totrov, Ruben Abagyan posted to blundell-group docking-algorithm docking-scoring-function energy-landscapes by bicko on 2005-09-23 01:06:30 as along with 2 people HawkinsJohnC cjeans

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