nickolay's library 242 articles Export

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	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
	The Protein Data Bank (PDB), Its Related Services and Software Tools as Key Components for In Silico Guided Drug Discovery [My Copy] J. Med. Chem. (1 November 2008) by Johannes Kirchmair, Patrick Markt, Simona Distinto, et al.Daniela Schuster, Gudrun M. Spitzer, Klaus R. Liedl, Thierry Langer, Gerhard Wolber posted to database pdb protein review structure by nickolay on 2009-01-13 18:59:57 as along with 2 people guhjy reyez
	Studies of protein-protein interfaces: a statistical analysis of the hydrophobic effect. [My Copy] Protein Sci, Vol. 6, No. 1. (January 1997), pp. 53-64. by C. J. Tsai, S. L. Lin, H. J. Wolfson, R. Nussinov posted to hyfrophobic-effect protein-interface protein-protein by nickolay on 2007-08-24 01:23:14 as along with 1 person bicko
	Towards Fully Automated Structure-based Function Prediction in Structural Genomics: A Case Study [My Copy] Journal of Molecular Biology, Vol. 367, No. 5. (13 April 2007), pp. 1511-1522. by James D. Watson, Steve Sanderson, Alexandra Ezersky, et al.Alexei Savchenko, Aled Edwards, Christine Orengo, Andrzej Joachimiak, Roman A. Laskowski, Janet M. Thornton posted to no-tag by nickolay on 2007-05-02 15:31:25 as along with 4 people and 2 groups ana tjimenez grottenolm jwm structural_bioinformatics Bioinformatics
	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
	Improvement in protein functional site prediction by distinguishing structural and functional constraints on protein family evolution using computational design. [My Copy] Nucleic Acids Res, Vol. 33, No. 18. (2005), pp. 5861-5867. by Gong Cheng, Bin Qian, Ram Samudrala, David Baker posted to to-be-tagged by nickolay on 2006-10-26 01:40:54 as along with 6 people and 3 groups bicko Einat marcius alexg sriram_s ladab structural_bioinformatics BioinfoCIPF SGU-CIPF
	An accurate, sensitive, and scalable method to identify functional sites in protein structures. [My Copy] Journal of molecular biology, Vol. 326, No. 1. (7 February 2003), pp. 255-261. by H. Yao, D. M. Kristensen, I. Mihalek, et al.M. E. Sowa, C. Shaw, M. Kimmel, L. Kavraki, O. Lichtarge posted to to-be-tagged by nickolay on 2006-03-01 19:11:47 as along with 5 people qluo chrn bicko beeblebrox sriram_s
	Automatic methods for predicting functionally important residues. [My Copy] J Mol Biol, Vol. 326, No. 4. (28 February 2003), pp. 1289-1302. by A. del Sol Mesa, F. Pazos, A. Valencia posted to to-be-tagged by nickolay on 2006-03-01 19:10:26 as along with 2 people kaarsinogen tjimenez
	Evolutionary predictions of binding surfaces and interactions. [My Copy] Curr Opin Struct Biol, Vol. 12, No. 1. (February 2002), pp. 21-27. by O. Lichtarge, M. E. Sowa posted to to-be-tagged by nickolay on 2006-03-01 19:09:14 as along with 1 person siebertm
	A new method to detect related function among proteins independent of sequence and fold homology. [My Copy] J Mol Biol, Vol. 323, No. 2. (18 October 2002), pp. 387-406. by S. Schmitt, D. Kuhn, G. Klebe posted to to-be-tagged by nickolay on 2006-02-12 01:37:47 as along with 1 person tjimenez
	A model for statistical significance of local similarities in structure. [My Copy] J Mol Biol, Vol. 326, No. 5. (7 March 2003), pp. 1307-1316. by A. Stark, S. Sunyaev, R. B. Russell posted to to-be-tagged by nickolay on 2005-12-16 21:16:30 as along with 8 people and 2 groups karbak ana nigham chad_davis thamelry robert scis0000001 siebertm structural_bioinformatics Bioinformatics
	Combining specificity determining and conserved residues improves functional site prediction [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (2009), 174. by Olga Kalinina, Mikhail Gelfand, Robert Russell posted to no-tag by nickolay on 2009-06-11 19:30:36 as along with 3 people and 1 group cdsouthan chocolate2009 AlexBateman Journal picks
	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
	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
	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
	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
	'Protein Peeling': an approach for splitting a 3D protein structure into compact fragments [My Copy] Bioinformatics, Vol. 22, No. 2. (15 January 2006), pp. 129-133. by Jean-Christophe Gelly, Alexandre G. de Brevern, Serge Hazout posted to to-be-tagged by nickolay on 2006-07-24 18:18:25 as along with 6 people and 4 groups ana barry dimka ttjoseph marcius choonpeng structural_bioinformatics Bioinformatics BioinfoCIPF SGU-CIPF
	Protein structure: geometry, topology and classification [My Copy] Reports of Progress in Physics, Vol. 64 (April 2001), pp. 517-590. by W. R. Taylor, A. C. W. May, N. P. Brown, A. Aszódi posted to domain-classification geometric-hashing graph-theory machine-learning msa pattern review structure-classification surface topology by nickolay on 2005-12-08 23:43:43 as
	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
	Recognition of spatial motifs in protein structures. [My Copy] J Mol Biol, Vol. 285, No. 4. (29 January 1999), pp. 1887-1897. by G. J. Kleywegt posted to algorithm application pattern by nickolay on 2005-12-08 23:11:18 as along with 2 people shadowman martainn
	PostDOCK: a structural, empirical approach to scoring protein ligand complexes. [My Copy] J Med Chem, Vol. 48, No. 22. (3 November 2005), pp. 6821-6831. by C. Springer, H. Adalsteinsson, M. M. Young, P. W. Kegelmeyer, D. C. Roe posted to application docking machine-learning pdb protein-ligand surface by nickolay on 2005-12-06 01:52:55 as along with 1 person and 2 groups sangeetha Bioinformatics insilicodrug
	An intuitive approach to measuring protein surface curvature. [My Copy] Proteins, Vol. 61, No. 4. (1 December 2005), pp. 1068-1074. by R. G. Coleman, M. A. Burr, D. L. Souvaine, A. C. Cheng posted to algorithm geometry-based surface by nickolay on 2005-12-06 01:49:34 as along with 2 people melo_mcr Evangelia
	An information theoretic approach to macromolecular modeling: I. Sequence alignments. [My Copy] Biophys J, Vol. 89, No. 5. (November 2005), pp. 2998-3007. by T. Aynechi, I. D. Kuntz posted to algorithm information-theory msa by nickolay on 2005-12-06 01:46:03 as along with 1 person and 2 groups marcius BioinfoCIPF SGU-CIPF
	Rapid Comparison of Protein Binding Site Surfaces with Property Encoded Shape Distributions [My Copy] Journal of Chemical Information and Modeling, Vol. 0, No. 0. (0000) by Sourav Das, Arshad Kokardekar, Curt M. Breneman posted to surface shape rapid comparison binding_site algorithm by nickolay on 2009-11-18 16:39:24 as
	Finding Key Members in Compound Libraries by Analyzing Networks of Molecules Assembled by Structural Similarity [My Copy] Journal of Chemical Information and Modeling, Vol. 0, No. 0. (30 October 0000), 091030094710018. by Zsolt Lepp, Chunfei Huang, Takashi Okada posted to similarity nov09 network molecule ligand compound_libraries cheminformatics by nickolay on 2009-11-03 20:39:55 as along with 1 person massivemayhem
	Docking Ligands into Flexible and Solvated Macromolecules. 5. Force-Field-Based Prediction of Binding Affinities of Ligands to Proteins [My Copy] Journal of Chemical Information and Modeling, Vol. 0, No. 0. (0000) by Pablo Englebienne, Nicolas Moitessier posted to solvent prediction nov09 ligand flexibility docking affinity by nickolay on 2009-11-03 20:35:14 as
	Identifying and Characterizing Binding Sites and Assessing Druggability [My Copy] Journal of Chemical Information and Modeling, Vol. 49, No. 2. (23 February 2009), pp. 377-389. by Thomas A. Halgren posted to no-tag by nickolay on 2009-08-19 15:58:47 as along with 4 people and 1 group richardbickerton TonyIvetac carlosjavierna timg McCammon
	Binding Site Similarity Analysis for the Functional Classification of the Protein Kinase Family [My Copy] Journal of Chemical Information and Modeling, Vol. 49, No. 2. (23 February 2009), pp. 318-329. by Sarah L. Kinnings, Richard M. Jackson posted to no-tag by nickolay on 2009-08-19 15:58:24 as along with 5 people mnishimu Klapampfer carlosjavierna jerome reyez
	GARD: A Generally Applicable Replacement for RMSD [My Copy] Journal of Chemical Information and Modeling, Vol. 49, No. 8. (24 August 2009), pp. 1889-1900. by J. Christian Baber, David C. Thompson, Jason B. Cross, Christine Humblet posted to sep09 by nickolay on 2009-08-19 15:37:16 as along with 3 people and 1 group A_Coletta_Thesis zimbo1 reyez Structural Biology Group TorVergata
	FINDSITE<sup>LHM</sup>: A Threading-Based Approach to Ligand Homology Modeling [My Copy] PLoS Comput Biol, Vol. 5, No. 6. (5 June 2009), e1000405. by Michal Brylinski, Jeffrey Skolnick posted to no-tag by nickolay on 2009-06-11 19:38:06 as along with 6 people and 2 groups phoenixzxl kshameer superpyrin reyez apaydin barry structural_bioinformatics McCammon
	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
	Residue frequencies and pairing preferences at protein-protein interfaces [My Copy] Proteins: Structure, Function, and Genetics, Vol. 43, No. 2. (2001), pp. 89-102. by Fabian Glaser, David M. Steinberg, Ilya A. Vakser, Nir Ben-Tal posted to aa-propensity binding-site-analysis protein-interface protein-protein p1 by nickolay on 2006-11-17 16:26:47 as along with 3 people Evangelia ladab timg
	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 scoring-functions review p2 docking by nickolay on 2006-02-23 21:49:56 as along with 25 people and 4 groups rabio ucbcjbm flbarroso csrocha oteri timg dgruiz cantupaz apaydin bicko chad_davis yongzhao ttjoseph ima sangeetha dgront blackbart gane5h mmuecke kazemi bpagano massivemayhem cjeans Evangelia nigham Structural Biology Group TorVergata Bioinformatics TSRI_MGL insilicodrug
	Structural characterization of proteins using residue environments. [My Copy] Proteins, Vol. 61, No. 4. (1 December 2005), pp. 741-747. by S. D. Mooney, M. H. Liang, R. DeConde, R. B. Altman posted to algorithm domain-classification pdb side-chains structure-classification by nickolay on 2005-12-16 16:29:55 as along with 1 person and 2 groups marcius BioinfoCIPF SGU-CIPF
	TESS: a geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites. [My Copy] Protein Sci, Vol. 6, No. 11. (November 1997), pp. 2308-2323. by A. C. Wallace, N. Borkakoti, J. M. Thornton posted to algorithm application geometric-hashing pdb structure-searching by nickolay on 2005-12-09 20:34:22 as along with 3 people shadowman tjimenez jwm
	The natural history of protein domains. [My Copy] Annu Rev Biophys Biomol Struct, Vol. 31 (2002), pp. 45-71. by C. P. Ponting, R. R. Russell posted to domain-classification review structure-function by nickolay on 2005-12-08 23:27:49 as along with 3 people BioNica ssgong IrinaMoreira
	Structure of Protein Interaction Networks and Their Implications on Drug Design [My Copy] PLoS Comput Biol, Vol. 5, No. 10. (30 October 2009), e1000550. by Takeshi Hase, Hiroshi Tanaka, Yasuhiro Suzuki, So Nakagawa, Hiroaki Kitano posted to protein-protein nov09 network drug by nickolay on 2009-11-03 20:45:42 as along with 9 people and 1 group kiekyon kshameer zwang phoenixzxl venancio CorinYeats ess30 poirel jbesnard Orengo Group Journal Picks
	3D-SURFER: software for high-throughput protein surface comparison and analysis [My Copy] Bioinformatics, Vol. 25, No. 21. (1 November 2009), pp. 2843-2844. by David La, Juan Esquivel-Rodriguez, Vishwesh Venkatraman, et al.Bin Li, Lee Sael, Stephen Ueng, Steven Ahrendt, Daisuke Kihara posted to surface software protein nov09 comparison by nickolay on 2009-10-23 17:57:57 as along with 3 people and 1 group operon kshameer renatomilani structural_bioinformatics
	Algorithms for optimal protein structure alignment [My Copy] Bioinformatics, Vol. 25, No. 21. (1 November 2009), pp. 2751-2756. by Aleksandar Poleksic posted to structure protein nov09 alignment algorithm by nickolay on 2009-10-23 17:56:15 as along with 5 people and 1 group barry operon kshameer kevinzheng1983 neils structural_bioinformatics
	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
	An Intersection Inequality Sharper than the Tanimoto Triangle Inequality for Efficiently Searching Large Databases [My Copy] Journal of Chemical Information and Modeling, Vol. 49, No. 8. (24 August 2009), pp. 1866-1870. by Pierre Baldi, Daniel S. Hirschberg posted to tanimoto similarity oct09 ligand cheminformatics by nickolay on 2009-10-07 01:36:53 as
	Structure of naphthoate synthase (MenB) from Mycobacterium tuberculosis in both native and product-bound forms. [My Copy] Acta crystallographica. Section D, Biological crystallography, Vol. 61, No. Pt 9. (September 2005), pp. 1199-1206. by Jodie M. Johnston, Vickery L. Arcus, Edward N. Baker posted to p2 by nickolay on 2009-09-10 19:42:18 as
	Crystal structure of the C47S mutant of human peroxiredoxin 5 [My Copy] Journal of Chemical Crystallography, Vol. 34, No. 8. (1 August 2004), pp. 553-558. by Christine Evrard, Aude Smeets, Bernard Knoops, Jean-Paul Declercq posted to p2 by nickolay on 2009-09-10 19:40:44 as
	Crystal Structure of the PTEN Tumor SuppressorImplications for Its Phosphoinositide Phosphatase Activity and Membrane Association [My Copy] Cell, Vol. 99, No. 3. (29 October 1999), pp. 323-334. by Jie-Oh Lee, Haijuan Yang, Maria-Magdalena Georgescu, et al.Antonio Di Cristofano, Tomohiko Maehama, Yigong Shi, Jack E. Dixon, Pier Pandolfi, Nikola P. Pavletich posted to p2 by nickolay on 2009-09-10 19:38:56 as
	Biophysical Studies of eIF4E Cap-binding Protein: Recognition of mRNA 5′ Cap Structure and Synthetic Fragments of eIF4G and 4E-BP1 Proteins [My Copy] Journal of Molecular Biology, Vol. 319, No. 3. (07 June 2002), pp. 615-635. by Anna Niedzwiecka, Joseph Marcotrigiano, Janusz Stepinski, et al.Marzena Jankowska-Anyszka, Aleksandra Wyslouch-Cieszynska, Michal Dadlez, Anne-Claude Gingras, Pawel Mak, Edward Darzynkiewicz, Nahum Sonenberg posted to p2 by nickolay on 2009-09-10 19:36:25 as
	Imidazo61,2-a9pyridines: A potent and selective class of cyclin-Dependent kinase inhibitors identified through structure-Based hybridisation [My Copy] Bioorganic & Medicinal Chemistry Letters, Vol. 13, No. 18. (September 2003), pp. 3021-3026. by M. Anderson posted to p2 by nickolay on 2009-09-10 19:35:05 as
	Free energy requirement for domain movement of an enzyme. [My Copy] The Journal of biological chemistry, Vol. 275, No. 25. (23 June 2000), pp. 18939-18945. by J. Ishijima, T. Nakai, S. Kawaguchi, K. Hirotsu, S. Kuramitsu posted to p2 by nickolay on 2009-09-10 19:33:55 as along with 1 person pablocarb

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p2	56
binding	47
protein	42
algorithm	35
protein-ligand	32
to-be-tagged	31
structure	29
site	28
prediction	25
bibtex-import	22
structure-function	17
surface	17
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docking	16
bsc	14
review	14
application	13
ligand	13
nov09	13
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p1	12
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alignment	10
comparison	10
binding-site-analysis	9
method	9
pattern	9
pdb	9
residue-conservation	9
aa-propensity	8
flexibility	8
moad	8
similarity	8
bs-similarity	7
wrmsd	7
hot-spots	6
drug	5
geometric-hashing	5
msa	5
props	5
scoring-functions	5
sep09	5
structure-searching	5
thermodynamics	5
amino-acids	4
cheminformatics	4
domain-classification	4
function	4
geometric	4
geometry-based	4
interaction	4
network	4
protein-interface	4
side-chains	4
software	4
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affinity	3
cadd	3
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graph-theory	3
lead_discovery	3
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printed	3
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small	3
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aug09	2
binding_site	2
chemistry	2
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clique	2
concavity	2
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insulin-sensitivity	2
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lead_optimization	2
machine-learning	2
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solvent	2
structural	2
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amber	1
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basal-glucose	1
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cmoparison	1
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gi	1
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hinge	1
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shape	1
simulation	1
tanimoto	1
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topology	1
visualization	1
web-based	1

nickolay's library 242 articles Export

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