nickolay's binding [47 articles] Export

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	Identification of protein functional surfaces by the concept of a split pocket [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 76, No. 4. (2009), pp. 959-976. by Yan Y. Tseng, Wen-Hsiung Li posted to site protein oct09 identification binding by nickolay on 2009-10-07 15:11:46 as along with 1 person and 1 group AliC Orengo Group Journal Picks
	QSAR Models for Predicting the Similarity in Binding Profiles for Pairs of Protein Kinases and the Variation of Models between Experimental Data Sets [My Copy] Journal of Chemical Information and Modeling, Vol. 49, No. 8. (24 August 2009), pp. 1974-1985. by Robert P. Sheridan, Kiyean Nam, Vladimir N. Maiorov, Daniel R. McMasters, Wendy D. Cornell posted to qsar oct09 kinase binding by nickolay on 2009-10-07 01:38:50 as
	Exploiting residue-level and profile-level interface propensities for usage in binding sites prediction of proteins [My Copy] BMC Bioinformatics, Vol. 8 (05 May 2007), 147. by Qiwen Dong, Xiaolong Wang, Lei Lin, Yi Guan posted to algorithm binding bsc interaction prediction props protein site by nickolay on 2009-03-29 17:40:36 as along with 4 people iaolier bicko zwang marti
	Partial Order Optimum Likelihood (POOL): Maximum Likelihood Prediction of Protein Active Site Residues Using 3D Structure and Sequence Properties [My Copy] PLoS Comput Biol, Vol. 5, No. 1. (16 January 2009), e1000266. by Wenxu Tong, Ying Wei, Leonel F. Murga, Mary J. Ondrechen, Ronald J. Williams posted to binding prediction protein site structure by nickolay on 2009-01-22 20:50:03 as
	Binding MOAD, a high-quality protein-ligand database. [My Copy] Nucleic Acids Res, Vol. 36, No. Database issue. (January 2008) by M. L. Benson, R. D. Smith, N. A. Khazanov, et al.B. Dimcheff, J. Beaver, P. Dresslar, J. Nerothin, H. A. Carlson posted to p2 binding database ligand moad protein by nickolay on 2009-01-21 20:42:40 as along with 6 people medic0747 pauldobson reyez massivemayhem higueruelo guhjy
	sc-PDB: an annotated database of druggable binding sites from the Protein Data Bank. [My Copy] J Chem Inf Model, Vol. 46, No. 2. (r 2006), pp. 717-727. by E. Kellenberger, P. Muller, C. Schalon, G. Bret, N. Foata, D. Rognan posted to binding bsc database drug ligand moad protein site by nickolay on 2008-08-27 15:49:30 as along with 6 people and 1 group BragilMassoud caporaso schlauchi daevans ramensky sim82 biomedical-nlp
	A simple and fuzzy method to align and compare druggable ligand-binding sites [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA. by Claire Schalon, Jean-Sébastien Surgand, Esther Kellenberger, Didier Rognan posted to algorithm binding bsc comparison fingerprint protein similarity site by nickolay on 2008-08-27 14:14:35 as along with 3 people tjimenez bicko willpitt
	Detection of 3D atomic similarities and their use in the discrimination of small molecule protein-binding sites [My Copy] Bioinformatics, Vol. 24, No. 16. (15 August 2008), pp. i105-111. by Rafael Najmanovich, Natalja Kurbatova, Janet Thornton posted to algorithm alignment binding bsc comparison graph site structure by nickolay on 2008-08-19 20:51:58 as along with 7 people iaolier krapnik ramensky apaydin tjimenez neils reyez
	Highly accurate method for ligand-binding site prediction in unbound state (apo) protein structures. [My Copy] Proteins (1 May 2008) by Mizuki Morita, Shugo Nakamura, Kentaro Shimizu posted to algorithm binding bsc ligand prediction protein site structure by nickolay on 2008-07-14 20:02:25 as
	How Different are Structurally Flexible and Rigid Binding Sites? Sequence and Structural Features Discriminating Proteins that Do and Do not Undergo Conformational Change upon Ligand Binding. [My Copy] J Mol Biol (29 September 2006) by Kannan Gunasekaran, Ruth Nussinov posted to binding bsc comparison flexibility protein review site structure by nickolay on 2008-07-08 15:05:37 as along with 10 people and 1 group aqeel reyez BragilMassoud dgruiz radestock lna yongzhao choonpeng weisblum higueruelo TSRI_MGL
	From the Similarity Analysis of Protein Cavities to the Functional Classification of Protein Families Using Cavbase [My Copy] Journal of Molecular Biology, Vol. 359, No. 4. (16 June 2006), pp. 1023-1044. by Daniel Kuhn, Nils Weskamp, Stefan Schmitt, Eyke Hullermeier, Gerhard Klebe posted to algorithm binding bsc comparison physicochemical similarity site by nickolay on 2008-07-08 15:03:05 as along with 2 people apaydin stege
	Analysis of binding site similarity, small-molecule similarity and experimental binding profiles in the human cytosolic sulfotransferase family. [My Copy] Bioinformatics, Vol. 23, No. 2. (15 January 2007) by R. J. Najmanovich, A. Allali-Hassani, R. J. Morris, et al.L. Dombrovsky, P. W. Pan, M. Vedadi, A. N. Plotnikov, A. Edwards, C. Arrowsmith, J. M. Thornton posted to binding bsc cmoparison protein review similarity site structure by nickolay on 2008-07-08 14:47:52 as along with 1 person grottenolm
	LigProf: A simple tool for in silico prediction of ligand-binding sites [My Copy] Journal of Molecular Modeling, Vol. 13, No. 3. (March 2007), pp. 445-455. by Koczyk, Grzegorz, Wyrwicz, Lucjan, Rychlewski, Leszek posted to binding bsc comparison prediction protein site structure by nickolay on 2008-07-08 14:38:30 as along with 1 person iaolier
	Do Structurally Similar Ligands Bind in a Similar Fashion? [My Copy] Journal of Medicinal Chemistry, Vol. 49, No. 23. (1 November 2006), pp. 6716-6725. by Jonas Bostrom, Anders Hogner, Stefan Schmitt posted to binding bsc comparison dds ligand protein similarity site structure by nickolay on 2008-07-08 14:24:45 as along with 4 people klexa schlauchi daevans superpyrin
	Structure-based identification of binding sites, native ligands and potential inhibitors for G-protein coupled receptors. [My Copy] Proteins, Vol. 51, No. 3. (15 May 2003), pp. 423-433. by C. N. Cavasotto, A. J. Orry, R. A. Abagyan posted to algorithm binding bsc flexibility gpcr method prediction protein site small by nickolay on 2008-07-08 14:04:41 as
	Comprehensive identification of "druggable" protein ligand binding sites. [My Copy] Genome Inform Ser Workshop Genome Inform, Vol. 15, No. 2. (2004), pp. 31-41. by J. An, M. Totrov, R. Abagyan posted to algorithm binding bsc de-novo physicochemical prediction protein site structure by nickolay on 2008-07-08 13:56:28 as along with 1 person sriram_s
	Searching for functional sites in protein structures. [My Copy] Current opinion in chemical biology, Vol. 8, No. 1. (February 2004), pp. 3-7. by S. Jones, J. M. Thornton posted to binding bsc function prediction protein review site structure by nickolay on 2008-06-10 19:06:59 as along with 7 people and 1 group qluo BragilMassoud LeightonP chrn Einat proteasome jwm structural_bioinformatics
	Large scale analysis of protein-binding cavities using self-organizing maps and wavelet-based surface patches to describe functional properties, selectivity discrimination, and putative cross-reactivity. [My Copy] Proteins, Vol. 71, No. 3. (15 May 2008), pp. 1288-1306. by Katrin Kupas, Alfred Ultsch, Gerhard Klebe posted to algorithm binding bsc comparison identification protein site by nickolay on 2007-12-04 21:17:45 as along with 4 people and 1 group rschulz sobolevnrm carlescorbi higueruelo baker-group
	On the nature of cavities on protein surfaces: Application to the identification of drug-binding sites [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 63, No. 4. (13 February 2006), pp. 892-906. by Murad Nayal, Barry Honig posted to binding classifier identification site small by nickolay on 2007-01-18 19:09:10 as along with 6 people and 1 group ubcg08l iaolier BragilMassoud pansapiens tjimenez Einat structural_bioinformatics
	Localization of binding sites in protein structures by optimization of a composite scoring function. [My Copy] Protein Sci, Vol. 15, No. 10. (October 2006), pp. 2366-2380. by A. Rossi, M. A. Marti-Renom, A. Sali posted to binding function localization printed protein scoring site structure by nickolay on 2007-01-18 19:05:03 as along with 3 people mkotlyar tjimenez MaggieYe
	LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation [My Copy] BMC Structural Biology, Vol. 6, No. 1. (24 September 2006), 19. by Bingding Huang, Michael Schroeder posted to algorithm binding geometric identification server site software by nickolay on 2007-01-18 18:58:13 as along with 6 people superpyrin tomjad iaolier richardbickerton reyez tjimenez
	Recognition of docking sites on a protein using [beta]-shape based on Voronoi diagram of atoms [My Copy] Computer-Aided Design, Vol. 38, No. 5. (May 2006), pp. 431-443. by Deok-Soo Kim, Cheol-Hyung Cho, Donguk Kim, Youngsong Cho posted to algorithm binding geometric identification protein site by nickolay on 2007-01-18 18:56:02 as
	Pattern recognition strategies for molecular surfaces: III. Binding site prediction with a neural network. [My Copy] J Comput Chem, Vol. 25, No. 6. (30 April 2004), pp. 779-789. by M. Keil, T. E. Exner, J. Brickmann posted to binding identification network neural prediction protein site surface by nickolay on 2007-01-18 18:51:41 as along with 1 person kaarsinogen
	Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites [My Copy] Bioinformatics, Vol. 21, No. 9. (1 May 2005), pp. 1908-1916. by Alasdair T. Laurie, Richard M. Jackson posted to binding method prediction printed protein site by nickolay on 2007-01-18 18:49:52 as along with 3 people tomjad ramiro2k sriram_s
	Fast prediction and visualization of protein binding pockets with PASS. [My Copy] J Comput Aided Mol Des, Vol. 14, No. 4. (May 2000), pp. 383-401. by G. P. Brady, P. F. Stouten posted to binding method prediction printed protein site visualization by nickolay on 2007-01-17 20:22:25 as along with 2 people tomjad tjimenez
	Characterization of protein-ligand interaction sites using experimental and computational methods. [My Copy] Current opinion in drug discovery & development, Vol. 9, No. 3. (May 2006), pp. 354-362. by Sandor Vajda, Frank Guarnieri posted to binding computational identification mapping mc review site solvent by nickolay on 2007-01-03 15:16:19 as along with 3 people and 1 group ubcg08l kentsis caporaso biomedical-nlp
	Identification and mapping of small-molecule binding sites in proteins: computational tools for structure-based drug design [My Copy] Il Farmaco, Vol. 57, No. 3. (1 March 2002), pp. 243-251. by Christoph Sotriffer, Gerhard Klebe posted to algorithm binding comparison indentification review site by nickolay on 2006-12-05 21:36:58 as
	LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins. [My Copy] J Mol Graph Model, Vol. 15, No. 6. (December 1997) by M. Hendlich, F. Rippmann, G. Barnickel posted to algorithm binding geometric identification site by nickolay on 2006-12-04 21:14:14 as along with 1 person tjimenez
	The automatic search for ligand binding sites in proteins of known three-dimensional structure using only geometric criteria. [My Copy] J Mol Biol, Vol. 256, No. 1. (16 February 1996), pp. 201-213. by K. P. Peters, J. Fauck, C. Frömmel posted to algorithm binding geometric identification site by nickolay on 2006-10-04 17:22:44 as along with 3 people ramiro2k tjimenez sriram_s
	The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure. [My Copy] J Comput Aided Mol Des, Vol. 8, No. 3. (June 1994), pp. 243-256. by H. J. Böhm posted to binding prediction protein-ligand scoring-functions thermodynamics by nickolay on 2006-08-25 18:36:32 as along with 4 people BragilMassoud nachtalp papatonyhill schlauchi
	A new method for estimating the importance of hydrophobic groups in the binding site of a protein. [My Copy] J Med Chem, Vol. 48, No. 4. (24 February 2005), pp. 1069-1078. by M. D. Kelly, R. L. Mancera posted to aa-propensity binding binding-site-analysis side-chains by nickolay on 2006-08-18 19:46:14 as along with 3 people and 2 groups barry blackbart ladab structural_bioinformatics Bioinformatics
	Protein-ligand interactions: exchange processes and determination of ligand conformation and protein-ligand contacts. [My Copy] Methods Enzymol, Vol. 239 (1994), pp. 657-700. by L. Y. Lian, I. L. Barsukov, M. J. Sutcliffe, K. H. Sze, G. C. Roberts posted to binding ligand protein-ligand structure-function by nickolay on 2006-08-18 18:53:54 as along with 1 person dgruiz
	Similarity networks of protein binding sites. [My Copy] Proteins, Vol. 62, No. 2. (1 February 2006), pp. 470-478. by Z. Zhang, M. G. Grigorov posted to binding clique protein-protein similarity-network by nickolay on 2006-01-20 20:27:43 as along with 1 person scis0000001
	Assessment of multiple binding modes in ligand-protein docking. [My Copy] J Med Chem, Vol. 47, No. 13. (17 June 2004), pp. 3334-3337. by P. Källblad, R. L. Mancera, N. P. Todorov posted to binding docking protein-ligand by nickolay on 2005-12-16 16:14:11 as along with 1 person nachtalp
	Supersites within superfolds. Binding site similarity in the absence of homology. [My Copy] Journal of molecular biology, Vol. 282, No. 4. (2 October 1998), pp. 903-918. by R. B. Russell, P. D. Sasieni, M. J. Sternberg posted to alignment binding domain-classification pdb protein-ligand structure-activity by nickolay on 2005-12-08 23:16:10 as along with 2 people martainn chad_davis
	Relibase: design and development of a database for comprehensive analysis of protein-ligand interactions. [My Copy] J Mol Biol, Vol. 326, No. 2. (14 February 2003), pp. 607-620. by M. Hendlich, A. Bergner, J. Günther, G. Klebe posted to application binding database moad pdb protein-ligand by nickolay on 2005-12-06 02:10:41 as along with 2 people blackbart massivemayhem
	Ligand-protein database: linking protein-ligand complex structures to binding data. [My Copy] J Med Chem, Vol. 44, No. 22. (25 October 2001), pp. 3592-3598. by O. Roche, R. Kiyama, C. L. Brooks posted to binding database protein-ligand by nickolay on 2005-12-06 02:06:34 as along with 2 people blackbart massivemayhem
	The PDBbind Database: Methodologies and Updates [My Copy] Journal of Medicinal Chemistry, Vol. 48, No. 12. (1 June 2005), pp. 4111-4119. by Renxiao Wang, Xueliang Fang, Yipin Lu, Chao-Yie Yang, Shaomeng Wang posted to binding database moad protein-ligand by nickolay on 2005-12-06 02:04:47 as along with 2 people reyez blackbart
	Computational tools for the analysis and visualization of multiple protein-ligand complexes [My Copy] Journal of Molecular Graphics and Modelling, Vol. 24, No. 3. (December 2005), pp. 186-194. by Sean E. O'Brien, David G. Brown, James E. Mills, Chris Phillips, Gregg Morris posted to aa-propensity algorithm application binding dd industry protein-ligand by nickolay on 2005-12-06 01:39:18 as along with 1 person and 1 group yongzhao TSRI_MGL
	Recognition of functional sites in protein structures. [My Copy] J Mol Biol, Vol. 339, No. 3. (Jun 2004), pp. 607-633. by Alexandra S. Peleg, Ruth Nussinov, Haim J. Wolfson posted to bibtex-import binding pattern structure-function by nickolay on 2005-12-05 16:20:45 as
	Predicting molecular interactions in silico: I. A guide to pharmacophore identification and its applications to drug design. [My Copy] Curr Med Chem, Vol. 11, No. 1. (Jan 2004), pp. 71-90. by Oranit Dror, Alexandra S. Peleg, Ruth Nussinov, Haim J. Wolfson posted to bibtex-import binding cadd dd pharmacophore prediction protein-ligand by nickolay on 2005-12-05 16:19:25 as
	From protein structure to biochemical function? [My Copy] J Struct Funct Genomics, Vol. 4, No. 2-3. (2003), pp. 167-177. by Roman A. Laskowski, James D. Watson, Janet M. Thornton posted to application bibtex-import binding prediction structure-function by nickolay on 2005-12-05 16:19:05 as
	Identification of protein functions from a molecular surface database, eF-site. [My Copy] J Struct Funct Genomics, Vol. 2, No. 1. (2002), pp. 9-22. by Kengo Kinoshita, Jun'ichi Furui, Haruki Nakamura posted to application bibtex-import binding clique database graph-theory structure-function surface by nickolay on 2005-12-05 16:18:20 as
	Unraveling hot spots in binding interfaces: progress and challenges. [My Copy] Curr Opin Struct Biol, Vol. 12, No. 1. (Feb 2002), pp. 14-20. by Warren L. Delano posted to bibtex-import binding hot-spots protein-protein review by nickolay on 2005-12-05 16:17:28 as
	Structural stability of binding sites: consequences for binding affinity and allosteric effects. [My Copy] Proteins, Vol. Suppl 4 (2000), pp. 63-71. by I. Luque, E. Freire posted to bibtex-import binding protein-ligand protein-protein structure-function thermodynamics by nickolay on 2005-12-05 16:15:31 as
	Conservation of polar residues as hot spots at protein interfaces. [My Copy] Proteins, Vol. 39, No. 4. (Jun 2000), pp. 331-342. by Z. Hu, B. Ma, H. Wolfson, R. Nussinov posted to bibtex-import binding hot-spots protein-protein residue-conservation by nickolay on 2005-12-05 16:15:20 as
	Anatomy of hot spots in protein interfaces. [My Copy] J Mol Biol, Vol. 280, No. 1. (Jul 1998), pp. 1-9. by A. A. Bogan, K. S. Thorn posted to bibtex-import binding hot-spots protein-interface structure-activity by nickolay on 2005-12-05 14:43:51 as

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p2	56
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protein	42
algorithm	34
protein-ligand	32
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structure	29
site	28
prediction	25
bibtex-import	22
structure-function	17
database	16
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surface	16
bsc	14
review	14
application	13
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nov09	13
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identification	11
alignment	10
binding-site-analysis	9
comparison	9
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residue-conservation	9
aa-propensity	8
flexibility	8
moad	8
similarity	8
bs-similarity	7
wrmsd	7
hot-spots	6
geometric-hashing	5
msa	5
props	5
scoring-functions	5
sep09	5
structure-searching	5
thermodynamics	5
amino-acids	4
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function	4
geometric	4
geometry-based	4
interaction	4
network	4
protein-interface	4
side-chains	4
software	4
structure-classification	4
affinity	3
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force-field	3
graph-theory	3
lead_discovery	3
molecular_dynamics	3
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printed	3
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small	3
superposition	3
aug09	2
chemistry	2
clique	2
concavity	2
dd	2
dds	2
information-theory	2
insulin	2
insulin-sensitivity	2
knowledge-based-potentials	2
lead_optimization	2
machine-learning	2
moe	2
molecule	2
physicochemical	2
similarity-network	2
solvent	2
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structural-conservation	2
structure-activity	2
virtual-screening	2
action	1
allostery	1
amber	1
aromatics	1
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beta-cells	1
binding_site	1
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biological_relevance	1
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charmm	1
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cmoparison	1
compound_libraries	1
computational	1
conservation	1
data	1
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distance	1
drug_discovery_and_development	1
electrostatics	1
energy_minimization	1
fingerprint	1
folding	1
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r	1
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tanimoto	1
target	1
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