nickolay's algorithm [34 articles] Export

Recent papers added to nickolay's library classified by the tag algorithm. You can also see everyone's algorithm.

	MISTRAL: a tool for energy-based multiple structural alignment of proteins [My Copy] Bioinformatics, Vol. 25, No. 20. (15 October 2009), pp. 2663-2669. by Cristian Micheletti, Henri Orland posted to software nov09 multiple_structural_alignment energy_minimization alignment algorithm by nickolay on 2009-11-03 21:08:02 as along with 2 people and 1 group jforment reyez Bioinformatics Core Service
	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
	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
	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
	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
	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
	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
	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
	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
	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
	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
	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
	Three-dimensional profiles: a new tool to identify protein surface similarities. [My Copy] J Mol Biol, Vol. 284, No. 4. (11 December 1998), pp. 1211-1221. by M. de Rinaldis, G. Ausiello, G. Cesareni, M. Helmer-Citterich posted to algorithm application msa pattern pdb structure-searching surface by nickolay on 2005-12-08 23:39:24 as along with 1 person dgront
	Annotation in three dimensions. PINTS: Patterns in Non-homologous Tertiary Structures. [My Copy] Nucleic Acids Res, Vol. 31, No. 13. (1 July 2003), pp. 3341-3344. by A. Stark, R. B. Russell posted to algorithm application pattern structure-function structure-searching by nickolay on 2005-12-08 23:30:47 as along with 2 people karbak 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
	MUSTA--a general, efficient, automated method for multiple structure alignment and detection of common motifs: application to proteins. [My Copy] J Comput Biol, Vol. 8, No. 2. (2001), pp. 93-121. by N. Leibowitz, R. Nussinov, H. J. Wolfson posted to algorithm geometric-hashing msa by nickolay on 2005-12-06 01:58:26 as
	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: II. Force Fields. [My Copy] Biophys J, Vol. 89, No. 5. (November 2005), pp. 3008-3016. by T. Aynechi, I. D. Kuntz posted to algorithm force-field information-theory by nickolay on 2005-12-06 01:47:19 as along with 1 person and 2 groups marcius BioinfoCIPF SGU-CIPF
	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
	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
	Generation and analysis of a protein-protein interface data set with similar chemical and spatial patterns of interactions. [My Copy] Proteins, Vol. 61, No. 1. (Oct 2005), pp. 6-20. by Shira Mintz, Alexandra S. Peleg, Haim J. Wolfson, Ruth Nussinov posted to algorithm application bibtex-import pattern protein-protein structure-function by nickolay on 2005-12-05 16:16:24 as
	ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information. [My Copy] Bioinformatics, Vol. 19, No. 1. (Jan 2003), pp. 163-164. by Fabian Glaser, Tal Pupko, Inbal Paz, et al.Rachel E. Bell, Dalit B. Shental, Eric Martz, Nir B. Tal posted to algorithm application bibtex-import protein-protein residue-conservation structure-function by nickolay on 2005-12-05 16:16:01 as
	Detection of protein three-dimensional side-chain patterns: new examples of convergent evolution. [My Copy] J Mol Biol, Vol. 279, No. 5. (Jun 1998), pp. 1211-1227. by R. B. Russell posted to aa-propensity algorithm alignment bibtex-import pattern structure-function by nickolay on 2005-12-05 16:14:38 as
	A graph-theoretic approach to the identification of three-dimensional patterns of amino acid side-chains in protein structures. [My Copy] J Mol Biol, Vol. 243, No. 2. (Oct 1994), pp. 327-344. by P. J. Artymiuk, A. R. Poirrette, H. M. Grindley, D. W. Rice, P. Willett posted to algorithm bibtex-import graph-theory pattern side-chains by nickolay on 2005-12-05 14:34:48 as

Note: You may cite this page as: http://www.citeulike.org/user/nickolay/tag/algorithm

p2	56
binding	47
protein	42
algorithm	34
protein-ligand	32
to-be-tagged	31
structure	29
site	28
prediction	25
bibtex-import	22
structure-function	17
database	16
docking	16
surface	16
bsc	14
review	14
application	13
ligand	13
nov09	13
protein-protein	13
p1	12
identification	11
alignment	10
binding-site-analysis	9
comparison	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
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
drug	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
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
structural	2
structural-conservation	2
structure-activity	2
virtual-screening	2
action	1
allostery	1
amber	1
aromatics	1
basal-glucose	1
beta-cells	1
binding_site	1
bioactivity	1
biological_relevance	1
calatytic	1
catalysis	1
charmm	1
classification	1
classifier	1
clustering	1
cmoparison	1
compound_libraries	1
computational	1
conservation	1
data	1
data-integration	1
de-novo	1
distance	1
drug_discovery_and_development	1
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
ligand-volume	1
localization	1
mapping	1
mc	1
metabolism	1
metabolome	1
metric	1
mining	1
model	1
multiple	1
multiple_structural_alignment	1
neural	1
ontology	1
opinion	1
package	1
pathway	1
pca	1
pharmacophore	1
property	1
python	1
qsar	1
r	1
residue	1
scoring	1
screening	1
server	1
simulation	1
tanimoto	1
target	1
topology	1
visualization	1
web-based	1

nickolay's algorithm [34 articles] Export

nickolay's tags