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	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
	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
	MSDsite: A database search and retrieval system for the analysis and viewing of bound ligands and active sites [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 58, No. 1. (2005), pp. 190-199. by Adel Golovin, Dimitris Dimitropoulos, Tom Oldfield, Abdelkrim Rachedi, Kim Henrick posted to database protein-ligand by nickolay on 2006-08-18 19:41:03 as along with 2 people and 1 group caporaso massivemayhem biomedical-nlp
	PDBLIG: Classification of Small Molecular Protein Binding in the Protein Data Bank [My Copy] J. Med. Chem., Vol. 47, No. 15. (15 July 2004), pp. 3807-3816. by A. J. Chalk, C. L. Worth, J. P. Overington, A. W. E. Chan posted to database protein-ligand by nickolay on 2006-08-18 19:04:14 as along with 2 people massivemayhem higueruelo
	Ligand Depot: a data warehouse for ligands bound to macromolecules [My Copy] Bioinformatics, Vol. 20, No. 13. (1 September 2004), pp. 2153-2155. by Zukang Feng, Li Chen, Himabindu Maddula, et al.Ozgur Akcan, Rose Oughtred, Helen M. Berman, John Westbrook posted to database protein-ligand by nickolay on 2006-08-18 19:03:05 as along with 5 people flbarroso reyez BragilMassoud nachtalp bicko
	Protein Ligand Database (PLD): additional understanding of the nature and specificity of protein-ligand complexes [My Copy] Bioinformatics, Vol. 19, No. 14. (22 September 2003), pp. 1856-1857. by Dushyanthan Puvanendrampillai, John B. Mitchell posted to database protein-ligand by nickolay on 2006-08-18 19:02:26 as along with 1 person massivemayhem
	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
	Surface motifs by a computer vision technique: Searches, detection, and implications for protein-ligand recognition [My Copy] Proteins: Structure, Function, and Genetics, Vol. 16, No. 3. (1993), pp. 278-292. by Daniel Fischer, Raquel Norel, Haim Wolfson, Ruth Nussinov posted to bs-similarity geometric-hashing method protein-ligand structure-function structure-searching by nickolay on 2006-06-29 22:39:15 as
	Fold Independent Structural Comparisons of Protein-Ligand Binding Sites for Exploring Functional Relationships [My Copy] Journal of Molecular Biology, Vol. 355, No. 5. (3 February 2006), pp. 1112-1124. by Nicola D. Gold, Richard M. Jackson posted to application bs-similarity database geometric-hashing moad protein-ligand structure-searching by nickolay on 2006-06-28 20:53:13 as
	Automated analysis of interatomic contacts in proteins [My Copy] Bioinformatics, Vol. 15, No. 4. (1 April 1999), pp. 327-332. by V. Sobolev, A. Sorokine, J. Prilusky, E. E. Abola, M. Edelman posted to application protein-ligand by nickolay on 2006-03-22 02:18:06 as along with 3 people dfdong bicko massivemayhem
	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
	LigBase: a database of families of aligned ligand binding sites in known protein sequences and structures. [My Copy] Bioinformatics, Vol. 18, No. 1. (January 2002), pp. 200-201. by A. C. Stuart, V. A. Ilyin, A. Sali posted to database moad protein-ligand by nickolay on 2006-03-02 02:22:14 as along with 1 person blackbart
	Structure-based virtual screening: an overview [My Copy] Drug Discovery Today, Vol. 7, No. 20. (15 October 2002), pp. 1047-1055. by Paul D. Lyne posted to cadd docking protein-ligand review virtual-screening by nickolay on 2006-02-23 21:55:26 as along with 2 people LamBras mmuecke
	Ligand binding: functional site location, similarity and docking [My Copy] Current Opinion in Structural Biology, Vol. 13, No. 3. (June 2003), pp. 389-395. by Stephen J. Campbell, Nicola D. Gold, Richard M. Jackson, David R. Westhead posted to bs-similarity docking protein-ligand review scoring-functions by nickolay on 2006-02-23 21:52:39 as
	A method for localizing ligand binding pockets in protein structures. [My Copy] Proteins, Vol. 62, No. 2. (1 February 2006), pp. 479-488. by F. Glaser, R. J. Morris, R. J. Najmanovich, R. A. Laskowski, J. M. Thornton posted to ligand-volume protein-ligand surface by nickolay on 2006-01-20 20:31:25 as along with 4 people tjimenez sriram_s bilab jwm
	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
	Classification and comparison of ligand-binding sites derived from grid-mapped knowledge-based potentials. [My Copy] J Mol Graph Model (27 October 2005) by Christian Hoppe, Christoph Steinbeck, Gerd Wohlfahrt posted to bs-similarity knowledge-based-potentials moe protein-ligand structure-classification by nickolay on 2006-01-20 20:21:30 as
	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
	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
	Recovering the true targets of specific ligands by virtual screening of the protein data bank. [My Copy] Proteins, Vol. 54, No. 4. (1 March 2004), pp. 671-680. by N. Paul, E. Kellenberger, G. Bret, P. Müller, D. Rognan posted to docking pdb protein-ligand virtual-screening by nickolay on 2005-12-06 02:12:24 as along with 2 people BragilMassoud insilico
	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
	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
	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
	Binding MOAD (Mother Of All Databases). [My Copy] Proteins, Vol. 60, No. 3. (Aug 2005), pp. 333-340. by Liegi Hu, Mark L. Benson, Richard D. Smith, Michael G. Lerner, Heather A. Carlson posted to protein-ligand pdb p2 p1 moad lab database bibtex-import by nickolay on 2005-12-05 16:20:57 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
	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
	Protein functional epitopes: hot spots, dynamics and combinatorial libraries. [My Copy] Curr Opin Struct Biol, Vol. 11, No. 3. (Jun 2001), pp. 364-369. by B. Ma, H. J. Wolfson, R. Nussinov posted to bibtex-import flexibility hot-spots protein-ligand residue-conservation structure-function by nickolay on 2005-12-05 16:15:43 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

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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
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printed	3
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small	3
superposition	3
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binding_site	2
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insulin-sensitivity	2
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folding	1
gi	1
gometry-based	1
gpcr	1
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hinge	1
hot_spots	1
hyfrophobic-effect	1
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itc	1
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ligand-volume	1
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mc	1
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server	1
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tanimoto	1
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nickolay's protein-ligand [32 articles] Export

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