nickolay's prediction [25 articles] Export

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

	Structure-Based Predictive Models for Allosteric Hot Spots [My Copy] PLoS Comput Biol, Vol. 5, No. 10. (9 October 2009), e1000531. by Omar N. A. Demerdash, Michael D. Daily, Julie C. Mitchell posted to structure prediction model hot_spots allostery by nickolay on 2009-11-04 16:08:16 as along with 3 people and 1 group apaydin klexa barry McCammon
	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
	Further development and validation of empirical scoring functions for structure-based binding affinity prediction [My Copy] Journal of Computer-Aided Molecular Design, Vol. 16, No. 1. (1 January 2002), pp. 11-26. by Renxiao Wang, Luhua Lai, Shaomeng Wang posted to scoring-functions prediction p2 affinity by nickolay on 2009-09-10 15:20:38 as along with 1 person GermanErlenkamp
	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
	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
	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
	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
	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
	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
	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
	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 fragment library based on Gaussian mixtures predicting favorable molecular interactions. [My Copy] J Mol Biol, Vol. 313, No. 1. (12 October 2001), pp. 197-214. by V. V. Rantanen, K. A. Denessiouk, M. Gyllenberg, T. Koski, M. S. Johnson posted to method prediction protein-ligand by nickolay on 2006-03-02 02:24:47 as along with 1 person tjimenez
	Finding important sites in protein sequences [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 99, No. 23. (12 November 2002), pp. 14764-14771. by Peter J. Bickel, Katherina J. Kechris, Philip C. Spector, Gary J. Wedemayer, Alexander N. Glazer posted to evolution prediction residue-conservation structure-function by nickolay on 2006-03-02 02:18:02 as along with 4 people qluo RebeccaHamer analogAI sriram_s
	An evolutionary trace method defines binding surfaces common to protein families. [My Copy] J Mol Biol, Vol. 257, No. 2. (29 March 1996), pp. 342-358. by O. Lichtarge, H. R. Bourne, F. E. Cohen posted to evolution prediction residue-conservation by nickolay on 2006-03-01 19:08:32 as along with 4 people and 1 group ramiro2k lna sriram_s cat_worth structural_bioinformatics
	Novel statistical-thermodynamic methods to predict protein-ligand binding positions using probability distribution functions. [My Copy] Proteins (14 November 2005) by A M M. Ruvinsky, A V V. Kozintsev posted to docking prediction protein-ligand thermodynamics by nickolay on 2006-01-20 20:24:52 as along with 1 person BragilMassoud
	Inferring Functional Relationships of Proteins from Local Sequence and Spatial Surface Patterns [My Copy] Journal of Molecular Biology, Vol. 332, No. 2. (12 September 2003), pp. 505-526. by Andrew T. Binkowski, Larisa Adamian, Jie Liang posted to bs-similarity gometry-based method pattern prediction protein-ligand structural-conservation structure-function by nickolay on 2005-12-16 19:26:06 as
	Progress in Modeling of Protein Structures and Interactions [My Copy] Science, Vol. 310, No. 5748. (28 October 2005), pp. 638-642. by Ora Schueler-Furman, Chu Wang, Phil Bradley, Kira Misura, David Baker posted to prediction review structure-function by nickolay on 2005-12-06 01:56:43 as along with 18 people and 3 groups krapnik rabio ucbcjbm paddydu flbarroso thaliana jwm vavi bicko KyuhoLee marcius eweaver tny dgront rsantana mirzazadeh insectopalo barry BioinfoCIPF SGU-CIPF structural_bioinformatics
	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
	Predicting molecular interactions in silico: II. Protein-protein and protein-drug docking. [My Copy] Curr Med Chem, Vol. 11, No. 1. (Jan 2004), pp. 91-107. by Dina S. Duhovny, Ruth Nussinov, Haim J. Wolfson posted to bibtex-import cadd docking prediction protein-ligand protein-protein review by nickolay on 2005-12-05 16:16:10 as

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

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
dds	2
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
structural-conservation	2
structure-activity	2
virtual-screening	2
action	1
allostery	1
amber	1
aromatics	1
basal-glucose	1
beta-cells	1
bioactivity	1
biological_relevance	1
calatytic	1
catalysis	1
charmm	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
mc	1
metabolism	1
metabolome	1
metric	1
mining	1
model	1
molecule	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
rapid	1
residue	1
scoring	1
screening	1
server	1
shape	1
simulation	1
tanimoto	1
target	1
topology	1
visualization	1
web-based	1

nickolay's prediction [25 articles] Export

nickolay's tags