nickolay's protein [42 articles] Export

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	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
	Alignment of multiple protein structures based on sequence and structure features. [My Copy] Protein engineering, design & selection : PEDS, Vol. 22, No. 9. (1 September 2009), pp. 569-574. by M. S. Madhusudhan, Benjamin M. Webb, Marc A. Marti-Renom, Narayanan Eswar, Andrej Sali posted to structure sep09 protein multiple alignment by nickolay on 2009-08-27 19:03:19 as along with 1 person dimka
	Use of Amino Acid Composition to Predict Ligand-Binding Sites [My Copy] Journal of Chemical Information and Modeling, Vol. 47, No. 2. (1 March 2007), pp. 400-406. by Shinji Soga, Hiroki Shirai, Masato Kobori, Noriaki Hirayama posted to amino-acids binding-site-analysis p1 protein protein-ligand structure surface by nickolay on 2009-08-06 19:01:15 as along with 1 person iaolier
	Propensities of polar and aromatic amino acids in noncanonical interactions: nonbonded contacts analysis of protein-ligand complexes in crystal structures. [My Copy] Journal of medicinal chemistry, Vol. 50, No. 6. (22 March 2007), pp. 1189-1196. by Yumi N. Imai, Yoshihisa Inoue, Yoshio Yamamoto posted to amino-acids aromatics p1 props protein protein-ligand structure by nickolay on 2009-08-06 17:15:31 as
	Understanding the Functional Roles of Amino Acid Residues in Enzyme Catalysis [My Copy] Journal of Molecular Biology, Vol. 390, No. 3. (17 July 2009), pp. 560-577. by Gemma L. Holliday, John B. O. Mitchell, Janet M. Thornton posted to amino-acids catalysis enzyme function p1 props protein residue-conservation by nickolay on 2009-08-06 16:36:41 as along with 4 people and 1 group bdessailly carlosjavierna ucbcjbm pablocarb Orengo Group Journal Picks
	Chemocavity: Specific Concavity in Protein Reserved for the Binding of Biologically Functional Small Molecules [My Copy] Journal of Chemical Information and Modeling, Vol. 48, No. 8. (1 August 2008), pp. 1679-1685. by Shinji Soga, Hiroki Shirai, Masato Kobori, Noriaki Hirayama posted to binding-site-analysis concavity p1 protein structure surface by nickolay on 2009-08-06 16:18:31 as
	Identification of the Druggable Concavity in Homology Models Using the PLB Index [My Copy] Journal of Chemical Information and Modeling, Vol. 47, No. 6. (1 November 2007), pp. 2287-2292. by Shinji Soga, Hiroki Shirai, Masato Kobori, Noriaki Hirayama posted to binding-site-analysis concavity identification p1 protein surface by nickolay on 2009-08-06 16:15:47 as
	Predicting Protein Function and Binding Profile via Matching of Local Evolutionary and Geometric Surface Patterns [My Copy] Journal of Molecular Biology, Vol. 387, No. 2. (27 March 2009), pp. 451-464. by Yan Y. Tseng, Joseph Dundas, Jie Liang posted to evolution function prediction protein structure by nickolay on 2009-04-01 15:47:21 as along with 3 people and 4 groups sobolevnrm pablocarb barry structural_bioinformatics McCammon Bioinformatics baker-group
	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
	Protein classification combining surface analysis and primary structure [My Copy] Protein Engineering, Design and Selection, Vol. 22, No. 4. (1 April 2009), pp. 267-272. by Loris Nanni, Saveria Mazzara, Linda Pattini, Alessandra Lumini posted to aa-propensity classification protein sequence structure surface by nickolay on 2009-03-20 16:34:17 as along with 1 person and 1 group sobolevnrm baker-group
	Using least median of squares for structural superposition of flexible proteins [My Copy] BMC Bioinformatics, Vol. 10 (22 January 2009), 29. by Yu-Shen, Karthik Ramani posted to protein structure superposition wrmsd by nickolay on 2009-01-22 20:51:50 as along with 2 people yxue reyez
	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
	Differences between High- and Low-Affinity Complexes of Enzymes and Nonenzymes. [My Copy] Journal of medicinal chemistry, Vol. 51 (1 October 2008), pp. 6432-6441. by Heather A. Carlson, Richard D. Smith, Nickolay A. Khazanov, Paul D. Kirchhoff, James B. Dunbar, Mark L. Benson posted to protein p2 p1 moad ligand enzyme affinity by nickolay on 2009-01-21 20:43:54 as along with 1 person higueruelo
	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
	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
	The Thermodynamics of Protein-Ligand Interaction and Solvation: Insights for Ligand Design. [My Copy] Journal of molecular biology (9 October 2008) by Tjelvar S G S. Olsson, Mark A A. Williams, William R R. Pitt, John E E. Ladbury posted to dds interaction itc ligand protein surface thermodynamics by nickolay on 2009-01-13 18:54:50 as along with 4 people and 1 group min013 higueruelo dfgreen barry McCammon
	Flexible protein alignment and hinge detection. [My Copy] Proteins, Vol. 48, No. 2. (1 August 2002), pp. 242-256. by Maxim Shatsky, Ruth Nussinov, Haim J. Wolfson posted to algorithm alignment flexibility hinge protein structure wrmsd by nickolay on 2008-09-07 17:31:30 as along with 2 people ubcg08l oteri
	Gaussian-weighted RMSD superposition of proteins: a structural comparison for flexible proteins and predicted protein structures. [My Copy] Biophys J, Vol. 90, No. 12. (15 June 2006), pp. 4558-4573. by K. L. Damm, H. A. Carlson posted to flexibility protein structure superposition wrmsd by nickolay on 2008-09-07 17:03:32 as along with 5 people mijam blackbart choonpeng rabio higueruelo
	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
	Protein structure alignment considering phenotypic plasticity [My Copy] Bioinformatics, Vol. 24, No. 16. (15 August 2008), pp. i98-104. by Gergely Csaba, Fabian Birzele, Ralf Zimmer posted to algorithm alignment flexibility protein similarity structure wrmsd by nickolay on 2008-08-19 20:53:48 as
	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
	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
	Optimization of multiple-sequence alignment based on multiple-structure alignment. [My Copy] Proteins, Vol. 62, No. 1. (1 January 2006), pp. 209-217. by M. Shatsky, R. Nussinov, H. J. Wolfson posted to algorithm alignment protein sequence structure wrmsd by nickolay on 2008-06-11 19:53:47 as
	3DCoffee: combining protein sequences and structures within multiple sequence alignments. [My Copy] J Mol Biol, Vol. 340, No. 2. (2 July 2004), pp. 385-395. by O. O'Sullivan, K. Suhre, C. Abergel, D. G. Higgins, C. Notredame posted to algorithm alignment protein sequence structure wrmsd by nickolay on 2008-06-11 19:49:44 as along with 4 people and 4 groups ana jwm analogAI edvin structural_bioinformatics Radiation_Damage Stressosome Bioinformatics
	Pairwise iterative superposition of distantly related proteins and assessment of the significance of 3-D structural similarity [My Copy] Protein Eng., Vol. 9, No. 12. (1 December 1996), pp. 1093-1101. by Alex C. May posted to algorithm protein structure superposition wrmsd by nickolay on 2008-06-11 19:42:10 as
	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
	Prediction of Protein-Protein Interaction Sites using Patch Analysis [My Copy] pp. 133-143. by S. Jones posted to interaction prediction props protein structure by nickolay on 2007-08-24 01:26:42 as
	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
	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
	Analysis of catalytic residues in enzyme active sites. [My Copy] J Mol Biol, Vol. 324, No. 1. (15 November 2002), pp. 105-121. by G. J. Bartlett, C. T. Porter, N. Borkakoti, J. M. Thornton posted to calatytic enzyme props protein site p1 by nickolay on 2006-03-02 02:19:36 as along with 4 people baaden gbart sriram_s siebertm

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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
database	16
docking	16
bsc	14
review	14
application	13
ligand	13
nov09	13
protein-protein	13
p1	12
identification	11
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
structure-classification	4
affinity	3
cadd	3
enzyme	3
evolution	3
force-field	3
graph-theory	3
lead_discovery	3
molecular_dynamics	3
oct09	3
printed	3
sequence	3
small	3
superposition	3
aug09	2
binding_site	2
chemistry	2
classification	2
clique	2
concavity	2
dd	2
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information-theory	2
insulin	2
insulin-sensitivity	2
knowledge-based-potentials	2
lead_optimization	2
machine-learning	2
mapping	2
moe	2
physicochemical	2
similarity-network	2
solvent	2
structural	2
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structure-activity	2
virtual-screening	2
action	1
allostery	1
amber	1
aromatics	1
basal-glucose	1
beta-cells	1
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charmm	1
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clustering	1
cmoparison	1
compound_libraries	1
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conservation	1
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distance	1
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electrostatics	1
energy_minimization	1
fingerprint	1
folding	1
gi	1
gometry-based	1
gpcr	1
graph	1
hinge	1
hot_spots	1
hyfrophobic-effect	1
indentification	1
industry	1
itc	1
kinase	1
lab	1
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mc	1
metabolism	1
metabolome	1
metric	1
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molecule	1
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ontology	1
opinion	1
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server	1
shape	1
simulation	1
tanimoto	1
target	1
topology	1
visualization	1
web-based	1

nickolay's protein [42 articles] Export

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