superpyrin's library 225 articles Export

	Protein-protein interaction hotspots carved into sequences. [My Copy] PLoS computational biology, Vol. 3, No. 7. (13 July 2007) by Yanay Ofran, Burkhard Rost posted to protein-protein by superpyrin on 2009-10-25 10:54:52 as along with 9 people and 2 groups qluo bicko dchughes grahamc cjeans zwang Jporci Pao-Yang higueruelo G4ID Genetics-of-Gambling
	SHARP2: protein-protein interaction predictions using patch analysis [My Copy] Bioinformatics, Vol. 22, No. 14. (15 July 2006), pp. 1794-1795. by Yoichi Murakami, Susan Jones posted to protein-protein by superpyrin on 2009-10-25 10:46:44 as along with 3 people flbarroso bicko ameetsoni
	An automated decision-tree approach to predicting protein interaction hot spots [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 68, No. 4. (1 September 2007), pp. 813-823. by Steven J. Darnell, David Page, Julie C. Mitchell posted to protein-protein by superpyrin on 2009-10-25 09:55:39 as along with 2 people bicko cjeans
	Structure-based method for analyzing protein–protein interfaces [My Copy] Journal of Molecular Modeling, Vol. 10, No. 1. (17 February 2004), pp. 44-54. by Ying Gao, Renxiao Wang, Luhua Lai posted to protein-protein by superpyrin on 2009-10-25 09:41:53 as
	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 surface binding-site by superpyrin on 2009-08-24 08:41:23 as along with 6 people tomjad iaolier richardbickerton reyez tjimenez nickolay
	Variable atomic radii for continuum-solvent electrostatics calculation. [My Copy] The Journal of chemical physics, Vol. 129, No. 1. (7 July 2008) by Baojing Zhou, Manish Agarwal, Chung F. Wong posted to atomic radii solvation by superpyrin on 2009-08-04 10:43:06 as along with 1 person onufriev
	Application of the Wang-Landau algorithm to the dimerization of glycophorin A. [My Copy] The Journal of chemical physics, Vol. 130, No. 21. (7 June 2009) by C. Gervais, T. Wüst, D. P. Landau, Y. Xu posted to folding by superpyrin on 2009-07-29 19:49:38 as
	Different binding modes of tropeines mediating inhibition and potentiation of alpha1 glycine receptors. [My Copy] Journal of neurochemistry, Vol. 109, No. 6. (June 2009), pp. 1725-1732. by G. Maksay, B. Laube, R. Schemm, J. Grudzinska, M. Drwal, H. Betz posted to gly-receptor by superpyrin on 2009-07-20 21:45:40 as
	E-novo: an automated workflow for efficient structure-based lead optimization. [My Copy] Journal of chemical information and modeling, Vol. 49, No. 7. (24 July 2009), pp. 1797-1809. by Bradley C. Pearce, David R. Langley, Jia Kang, Hongwei Huang, Amit Kulkarni posted to leadopt by superpyrin on 2009-07-01 09:14:14 as along with 1 person oteri
	Flexible Alignment of Small Molecules [My Copy] Journal of Medicinal Chemistry, Vol. 44, No. 10. (1 May 2001), pp. 1483-1490. by Paul Labute, Chris Williams, Miklos Feher, Elizabeth Sourial, Jonathan M. Schmidt posted to pharmacophore superposition by superpyrin on 2009-06-25 12:29:13 as
	ShaEP: Molecular Overlay Based on Shape and Electrostatic Potential [My Copy] Journal of Chemical Information and Modeling, Vol. 49, No. 2. (23 February 2009), pp. 492-502. by Mikko J. Vainio, Santeri J. Puranen, Mark S. Johnson posted to pharmacophore superposition by superpyrin on 2009-06-25 12:22:22 as along with 3 people and 1 group ubcg08l sobolevnrm sschurer baker-group
	Structure and function of the cerebral cortex [My Copy] Current Biology, Vol. 17, No. 12. (2007), pp. 443-449. by Stewart Shipp posted to brain by superpyrin on 2009-06-22 08:56:07 as
	The columnar organization of the neocortex. [My Copy] Brain, Vol. 120 ( Pt 4) (April 1997), pp. 701-722. by V. B. Mountcastle posted to brain by superpyrin on 2009-06-22 08:51:02 as along with 1 person and 1 group edauce ANR_MAPS
	Variac: an Autogenous Cognitive Architecture [My Copy] (2008) by Storss J. Hall posted to agi by superpyrin on 2009-06-22 08:34:57 as
	A Gentle Introduction to The Universal Algorithmic Agent AIXI [My Copy] (2003) by Marcus Hutter posted to agi by superpyrin on 2009-06-22 08:30:04 as along with 1 person robotact
	Analogy in a general-purpose reasoning system [My Copy] Cognitive Systems Research, Vol. 10, No. 3. (September 2009), pp. 286-296. by Pei Wang posted to agi artificial-intelligence nars by superpyrin on 2009-06-22 08:20:02 as
	Novel approach to structure-based pharmacophore search using computational geometry and shape matching techniques. [My Copy] Journal of chemical information and modeling, Vol. 48, No. 4. (April 2008), pp. 889-901. by J. O. Ebalunode, Z. Ouyang, J. Liang, W. Zheng posted to pharmacophore by superpyrin on 2009-06-14 08:34:29 as
	Structure-Based Shape Pharmacophore Modeling for the Discovery of Novel Anesthetic Compounds [My Copy] Bioorganic & Medicinal Chemistry (29 May 2009) by Jerry O. Ebalunode, Xialan Dong, Zheng Ouyang, Jie Liang, Roderic G. Eckenhoff, Weifan Zheng posted to pharmacophore scoring by superpyrin on 2009-06-14 08:24:40 as
	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 docking by superpyrin on 2009-06-10 08:08:01 as along with 6 people and 2 groups phoenixzxl nickolay kshameer reyez apaydin barry structural_bioinformatics McCammon
	GSK-3: tricks of the trade for a multi-tasking kinase. [My Copy] J Cell Sci, Vol. 116, No. Pt 7. (1 April 2003), pp. 1175-1186. by B. W. Doble, J. R. Woodgett posted to gsk3 by superpyrin on 2009-06-08 08:25:53 as along with 1 person guhjy
	Pharmacological inhibitors of glycogen synthase kinase 3. [My Copy] Trends Pharmacol Sci, Vol. 25, No. 9. (September 2004), pp. 471-480. by L. Meijer, M. Flajolet, P. Greengard posted to gsk3 by superpyrin on 2009-06-08 08:17:48 as along with 1 person guhjy
	The renaissance of GSK3 [My Copy] Nat Rev Mol Cell Biol, Vol. 2, No. 10. (October 2001), pp. 769-776. by Philip Cohen, Sheelagh Frame posted to gsk3 by superpyrin on 2009-06-08 08:05:36 as
	Fpocket: An open source platform for ligand pocket detection [My Copy] BMC Bioinformatics, Vol. 10 (02 June 2009), 168. by Vincent Le Guilloux, Peter Schmidtke, Pierre Tuffery posted to binding-site by superpyrin on 2009-06-07 13:35:05 as along with 2 people sobolevnrm reyez
	Improving the Quality of 3D-QSAR by Using Flexible-Ligand Receptor Models [My Copy] Journal of Chemical Information and Modeling, Vol. 45, No. 6. (1 November 2005), pp. 1920-1933. by Jianfeng Pei, Hao Chen, Zhenming Liu, et al.Xiaofeng Han, Qi Wang, Bin Shen, Jiaju Zhou, Luhua Lai posted to flexible pseudoreceptor qsar by superpyrin on 2009-06-07 09:19:23 as
	VASCo: computation and visualization of annotated protein surface contacts [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (2009), 32. by Georg Steinkellner, Robert Rader, Gerhard Thallinger, Christoph Kratky, Karl Gruber posted to pymol surface by superpyrin on 2009-06-02 08:36:00 as along with 5 people richardbickerton higueruelo kshameer neils svozil
	Robust optimization of scoring functions for a target class [My Copy] Journal of Computer-Aided Molecular Design by Markus Seifert posted to docking scoring by superpyrin on 2009-05-31 09:36:47 as
	Community-wide assessment of GPCR structure modelling and ligand docking: GPCR Dock 2008. [My Copy] Nature reviews. Drug discovery (22 May 2009) by Mayako Michino, Enrique Abola, Gpcr Dock D. 2008 Participants, et al.Charles L L. Brooks, J Scott S. Dixon, John Moult, Raymond C C. Stevens posted to docking gpcr by superpyrin on 2009-05-24 13:34:51 as along with 1 person sschurer
	Distribution of Distinguishable Objects to Bins: Generating All Distributions [My Copy] In Procceedings of WALCOM 2007 (2007), pp. 136-150. by M. A. Adnan, S. Rahman posted to algorithm combinatorial by superpyrin on 2009-05-24 13:14:24 as
	SeleX-CS: A New Consensus Scoring Algorithm for Hit Discovery and Lead Optimization [My Copy] Journal of Chemical Information and Modeling, Vol. 49, No. 3. (23 March 2009), pp. 623-633. by Shay Bar-Haim, Ayelet Aharon, Tal Ben-Moshe, Yael Marantz, Hanoch Senderowitz posted to eben qsar selex by superpyrin on 2009-05-23 21:09:59 as
	Outsourcing lead optimization: constant change is here to stay [My Copy] Drug Discovery Today, Vol. 12, No. 1-2. (January 2007), pp. 62-70. by D. Clark posted to business development leadopt by superpyrin on 2009-05-19 08:02:48 as
	Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation. [My Copy] J Comput Chem, Vol. 23, No. 16. (December 2002), pp. 1623-1641. by A. Jakalian, D. B. Jack, C. I. Bayly posted to charges by superpyrin on 2009-05-13 10:33:00 as along with 3 people and 1 group lillekatt patricia sobolevnrm baker-group
	Identification of Novel Glycogen Synthase Kinase-3beta Substrate-interacting Residues Suggests a Common Mechanism for Substrate Recognition [My Copy] J. Biol. Chem., Vol. 281, No. 41. (13 October 2006), pp. 30621-30630. by Ronit Ilouz, Noga Kowalsman, Miriam Eisenstein, Hagit Eldar-Finkelman posted to gsk3 kinase by superpyrin on 2009-05-05 20:43:35 as
	Specific modulation of protein kinase activity via small peptides. [My Copy] Regulatory peptides (16 December 2008) by Helio Miranda M. Costa-Junior, Mariana J J. Suetsugu, José Eduardo E. Krieger, Deborah Schechtman posted to kinase by superpyrin on 2009-05-05 13:46:40 as along with 1 person higueruelo
	Internal coarse-graining of molecular systems [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 16. (21 April 2009), pp. 6453-6458. by Jérôme Feret, Vincent Danos, Jean Krivine, Russ Harmer, Walter Fontana posted to biology systems by superpyrin on 2009-05-05 08:46:34 as along with 9 people and 1 group jvb leemond31 Scis0000002 reyez trfield sobolevnrm paulschlesinger jjray kshundyak baker-group
	Fuzzy Pharmacophore Models from Molecular Alignments for Correlation-Vector-Based Virtual Screening [My Copy] Journal of Medicinal Chemistry, Vol. 47, No. 19. (1 September 2004), pp. 4653-4664. by Steffen Renner, Gisbert Schneider posted to pharmacophore screening by superpyrin on 2009-05-04 10:01:20 as
	Scaffold hopping by "fuzzy" pharmacophores and its application to RNA targets. [My Copy] Chembiochem, Vol. 8, No. 16. (5 November 2007), pp. 1932-1936. by Y. Tanrikulu, M. Nietert, U. Scheffer, et al.E. Proschak, K. Grabowski, P. Schneider, M. Weidlich, M. Karas, M. Göbel, G. Schneider posted to pharmacophore by superpyrin on 2009-05-04 09:52:23 as along with 1 person apostola
	Structure-Based Pharmacophore Screening for Natural-Product-Derived PPARgamma Agonists [My Copy] ChemBioChem, Vol. 10, No. 1. (2009), pp. 75-78. by Yusuf Tanrikulu, Oliver Rau, Oliver Schwarz, et al.Ewgenij Proschak, Karsten Siems, Lutz Müller-Kuhrt, Manfred Schubert-Zsilavecz, Gisbert Schneider posted to pharmacophore ppar screening by superpyrin on 2009-05-04 09:46:58 as
	Peptides Targeting Protein Kinases: Strategies and Implications [My Copy] Physiology, Vol. 21 (2006), pp. 411-418. by Oksana Kaidanovich-Beilin, Hagit Eldar-Finkelman posted to gsk3 kinase by superpyrin on 2009-05-03 21:33:11 as
	ParaFrag—an approach for surface-based similarity comparison of molecular fragments [My Copy] Journal of Molecular Modeling, Vol. 14, No. 7. (31 July 2008), pp. 547-558. by Arjen-Joachim Jakobi, Harald Mauser, Timothy Clark posted to leadopt pharmacophore by superpyrin on 2009-04-18 12:51:12 as along with 1 person allmensch
	Efficient Drug Lead Discovery and Optimization [My Copy] Accounts of Chemical Research, Vol. 0, No. 0. (0000) by William L. Jorgensen posted to leadopt by superpyrin on 2009-04-17 19:48:40 as along with 6 people and 2 groups nanonan tbinbal Thermaneutist jmccammon sschurer sobolevnrm McCammon baker-group
	Derivation of Preliminary Three-Dimensional Pharmacophores for Nonhalogenated Volatile Anesthetics [My Copy] Anesth Analg, Vol. 99, No. 3. (1 September 2004), pp. 744-751. by Jason C. Sewell, John W. Sear posted to pharmacophore by superpyrin on 2009-04-03 20:57:46 as
	Metabolic control analysis: a survey of its theoretical and experimental development. [My Copy] The Biochemical journal, Vol. 286 ( Pt 2) (1 September 1992), pp. 313-330. by D. A. Fell posted to biology systems by superpyrin on 2009-03-24 07:50:35 as along with 2 people michaelbarton csanford
	The challenges of modeling mammalian biocomplexity [My Copy] Nat Biotech, Vol. 22, No. 10. (October 2004), pp. 1268-1274. by Jeremy K. Nicholson, Elaine Holmes, John C. Lindon, Ian D. Wilson posted to biology systems by superpyrin on 2009-03-23 08:01:19 as along with 3 people rklancer balicea fishtank
	Metabolic control analysis to identify optimal drug targets [My Copy] Systems Biological Approaches in Infectious Diseases (2007), pp. 171-189. by Jorrit Hornberg, Frank Bruggeman, Barbara Bakker, Hans Westerhoff posted to biology systems by superpyrin on 2009-03-23 07:56:27 as
	Systematic discovery of multicomponent therapeutics. [My Copy] Proc Natl Acad Sci U S A, Vol. 100, No. 13. (24 June 2003), pp. 7977-7982. by A. A. Borisy, P. J. Elliott, N. W. Hurst, et al.M. S. Lee, J. Lehar, E. R. Price, G. Serbedzija, G. R. Zimmermann, M. A. Foley, B. R. Stockwell, C. T. Keith posted to biology systems by superpyrin on 2009-03-23 07:41:48 as along with 4 people yprassas rmk aheilbut Borelli
	Biological robustness. [My Copy] Nature reviews. Genetics, Vol. 5, No. 11. (November 2004), pp. 826-837. by Hiroaki Kitano posted to biology systems by superpyrin on 2009-03-23 07:39:09 as along with 16 people and 5 groups VGreiff sergiun dbk betainverse korakot LeightonP monod bayesian teuder biosv madhadron nickluscombe anatiferous timflutre ekoenig tomhebbron streptomyces Philosophy_of_Information dbk-lab Blog_and_Wiki_Research EBI-regulation
	Hot-Spots-Guided Receptor-Based Pharmacophores (HS-Pharm): A Knowledge-Based Approach to Identify Ligand-Anchoring Atoms in Protein Cavities and Prioritize Structure-Based Pharmacophores [My Copy] Journal of Chemical Information and Modeling, Vol. 48, No. 7. (1 July 2008), pp. 1396-1410. by Caterina Barillari, Gilles Marcou, Didier Rognan posted to pharmacophore by superpyrin on 2009-03-17 11:14:43 as along with 3 people xdeupi tbinbal higueruelo
	Pharao: pharmacophore alignment and optimization. [My Copy] Journal of molecular graphics & modelling, Vol. 27, No. 2. (September 2008), pp. 161-169. by J. Taminau, G. Thijs, H. De Winter posted to pharmacophore by superpyrin on 2009-03-17 10:22:36 as
	Global mapping of pharmacological space [My Copy] Nature Biotechnology, Vol. 24, No. 7. (13 July 2006), pp. 805-815. by Gaia V. Paolini, Richard H. B. Shapland, Willem P. van Hoorn, Jonathan S. Mason, Andrew L. Hopkins posted to biology systems by superpyrin on 2009-03-05 14:27:57 as along with 12 people and 1 group bertelsen sameersoi richardbickerton ramensky Yanno BragilMassoud guhjy kuhn bicko caporaso allmensch jerome_ucsf_slb biomedical-nlp
	A robustness-based approach to systems-oriented drug design [My Copy] Nat Rev Drug Discov, Vol. 6, No. 3. (23 March 2007), pp. 202-210. by Hiroaki Kitano posted to biology systems by superpyrin on 2009-03-05 14:23:35 as along with 4 people abhishek_tiwari bicko massivemayhem higueruelo

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herg	27
superposition	21
gpcr	20
cytochrome	18
3a4	14
binding	14
pharmacophore	14
docking	11
p2x	11
conformations	10
p450	10
artificial-intelligence	9
2d6	8
biology	8
nonbond	8
systems	8
screening	7
kinase	6
quorum-sensing	6
folding	5
gsk3	5
induction	5
leadopt	5
cation-pi	4
protein-protein	4
pxr	4
admet	3
agi	3
bbb	3
cystic-fibrosis	3
hbond	3
qsar	3
atpase	2
auction	2
binding-site	2
brain	2
hydrophobic-interaction	2
lipophilicity	2
membrane-protein	2
review	2
scoring	2
selectivity	2
surface	2
algorithm	1
atomic	1
business	1
charges	1
combinatorial	1
development	1
eben	1
flexible	1
fragment	1
gly-receptor	1
hydration	1
ion-channel	1
knowledge-representation	1
mchr1	1
metasite	1
mif	1
nars	1
pgp	1
pka	1
ppar	1
pseudoreceptor	1
pymol	1
qm-drug-discovery	1
radii	1
rna	1
selex	1
solvation	1
synthetase	1

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