massivemayhem's library 277 articles Export

	Finding Key Members in Compound Libraries by Analyzing Networks of Molecules Assembled by Structural Similarity [My Copy] Journal of Chemical Information and Modeling, Vol. 0, No. 0. (30 October 0000), 091030094710018. by Zsolt Lepp, Chunfei Huang, Takashi Okada posted to chemical_networks chemical_libraries chemical_biology by massivemayhem on 2009-11-05 10:53:52 as along with 1 person nickolay
	Geometry of nonbonded interactions involving planar groups in proteins [My Copy] Progress in Biophysics and Molecular Biology, Vol. 95, No. 1-3. (September 2007), pp. 83-137. by Pinak Chakrabarti, Rajasri Bhattacharyya posted to interactions credo by massivemayhem on 2009-09-02 16:49:33 as along with 1 person ubcg08l
	Structural artifacts in protein-ligand X-ray structures: implications for the development of docking scoring functions. [My Copy] Journal of medicinal chemistry, Vol. 52, No. 18. (24 September 2009), pp. 5673-5684. by Chresten R. Søndergaard, Alison Elizabeth E. Garrett, Tommy Carstensen, Gianluca Pollastri, Jens Erik E. Nielsen posted to pdbbind crystallography by massivemayhem on 2009-09-01 20:50:40 as along with 1 person skoddet
	LigMatch: A Multiple Structure-Based Ligand Matching Method for 3D Virtual Screening [My Copy] Journal of Chemical Information and Modeling, Vol. 0, No. 0. (0000) by Sarah L. Kinnings, Richard M. Jackson posted to virtual-screening by massivemayhem on 2009-08-26 14:59:43 as along with 1 person reyez
	Halogen Bonding - A Novel Interaction for Rational Drug Design? [My Copy] Journal of Medicinal Chemistry, Vol. 52, No. 9. (14 May 2009), pp. 2854-2862. by Yunxiang Lu, Ting Shi, Yong Wang, et al.Huaiyu Yang, Xiuhua Yan, Xiaoming Luo, Hualiang Jiang, Weiliang Zhu posted to halogen-bond by massivemayhem on 2009-08-25 16:52:45 as along with 2 people higueruelo jerome
	‘Metabolite-likeness’ as a criterion in the design and selection of pharmaceutical drug libraries [My Copy] Drug Discovery Today, Vol. 14, No. 1-2. (28 January 2009), pp. 31-40. by P. Dobson, Y. Patel, D. Kell posted to drug-design metabolites by massivemayhem on 2009-07-15 14:40:26 as along with 9 people mingzhi richardbickerton vpenelle jmuhlich lptolik pauldobson sschurer egonw dullhunk
	Unconventional 2D Shape Similarity Method Affords Comparable Enrichment as a 3D Shape Method in Virtual Screening Experiments [My Copy] Journal of Chemical Information and Modeling, Vol. 0, No. 0. (0000) by Jerry O. Ebalunode, Weifan Zheng posted to ligand-based-virtual-screening ligand-shapes shape-similarity by massivemayhem on 2009-06-23 17:25:38 as along with 1 person ima
	Carbonyl-Carbonyl Interactions can be Competitive with Hydrogen Bonds [My Copy] Acta Crystallographica Section B, Vol. 54, No. 3. (Jun 1998), pp. 320-329. by F. H. Allen, C. A. Baalham, J. P. M. Lommerse, P. R. Raithby posted to carbonyl-interactions by massivemayhem on 2009-05-29 09:51:03 as
	The Weak Hydrogen Bond In Structural Chemistry and Biology [My Copy] Journal of the American Chemical Society In The Weak Hydrogen Bond In Structural Chemistry and Biology, Vol. 9, No. 1. (1 January 2001), pp. 191-192. by G. R. Desiraju, Thomas Steiner posted to weak-hbonds by massivemayhem on 2009-05-29 09:41:12 as
	Novel Method for the Evaluation of 3D Conformation Generators [My Copy] Journal of Chemical Information and Modeling, Vol. 0, No. 0. (0000) by Terufumi Takagi, Michiko Amano, Masaki Tomimoto posted to conformers by massivemayhem on 2009-05-14 13:50:07 as along with 2 people reyez alfons
	Position Specific Interaction Dependent Scoring Technique for Virtual Screening Based on Weighted Protein−Ligand Interaction Fingerprint Profiles [My Copy] Journal of Chemical Information and Modeling, Vol. 49, No. 5. (22 May 2009), pp. 1185-1192. by Ravi K. Nandigam, Sangtae Kim, Juswinder Singh, Claudio Chuaqui posted to clustering protein-ligand sift by massivemayhem on 2009-05-08 09:57:53 as along with 3 people ucbcjbm bio_dataminer sschurer
	The Hydrogen Bond in the Solid State [My Copy] Angewandte Chemie International Edition, Vol. 41, No. 1. (2002), pp. 48-76. by Thomas Steiner posted to hydrogen-bonding by massivemayhem on 2009-05-06 10:08:03 as
	Better than Random? The Chemotype Enrichment Problem. [My Copy] Journal of chemical information and modeling (27 April 2009) by Mark D D. Mackey, James L L. Melville posted to enrichment-factor virtual-screening by massivemayhem on 2009-05-01 11:44:53 as along with 1 person reyez
	Kinase inhibitors and the case for CH..O hydrogen bonds in protein-ligand binding [My Copy] Proteins: Structure, Function, and Genetics, Vol. 49, No. 4. (2002), pp. 567-576. by Albert C. Pierce, Kathryn L. Sandretto, Guy W. Bemis posted to hydrogen-bonding protein-ligand weak-hbonds by massivemayhem on 2009-04-30 16:09:44 as
	How to do an evaluation: pitfalls and traps. [My Copy] J Comput Aided Mol Des (23 January 2008) by Paul C. Hawkins, Gregory L. Warren, A G. Skillman, Anthony Nicholls posted to crystallography docking by massivemayhem on 2009-04-08 13:39:16 as along with 3 people BragilMassoud LamBras thanatos
	Hydrogen Bonding and π-Stacking: How Reliable are Force Fields? A Critical Evaluation of Force Field Descriptions of Nonbonded Interactions [My Copy] Journal of Chemical Information and Modeling, Vol. 0, No. 0. (0000) by Robert S. Paton, Jonathan M. Goodman posted to force-field protein-ligand by massivemayhem on 2009-04-01 15:10:24 as along with 2 people middledomain carlosjavierna
	Prediction of HIV-1 protease inhibitor resistance by Molecular Modeling Protocols (MMPs) using GenMol(TM) software [My Copy] European Journal of Medicinal Chemistry, Vol. In Press, Corrected Proof by G. Pèpe, J. Courcambeck, R. Perbost, P. Jouanna, P. Halfon posted to drug-resistance molecular-modelling by massivemayhem on 2009-03-03 13:21:17 as along with 1 person joseph_x_zhou
	Accelerating molecular dynamic simulation on graphics processing units [My Copy] Journal of Computational Chemistry, Vol. 30, No. 6. (2009), pp. 864-872. by Mark S. Friedrichs, Peter Eastman, Vishal Vaidyanathan, et al.Mike Houston, Scott Legrand, Adam L. Beberg, Daniel L. Ensign, Christopher M. Bruns, Vijay S. Pande posted to cuda gpu molecular-dynamics nvidia by massivemayhem on 2009-02-08 11:54:34 as along with 10 people and 3 groups anuragsethi kevinchannon flbarroso r2s2 iantunbridge ihaque sobolevnrm ruvido barry RamuAnandakrishnan baker-group structural_bioinformatics McCammon
	The importance of discerning shape in molecular pharmacology. [My Copy] Trends in pharmacological sciences (31 January 2009) by Sandhya Kortagere, Matthew D D. Krasowski, Sean Ekins posted to ligand-shapes by massivemayhem on 2009-02-04 17:25:07 as along with 2 people tbinbal higueruelo
	Ultrafast shape recognition: Evaluating a new ligand-based virtual screening technology [My Copy] Journal of Molecular Graphics and Modelling, Vol. 27, No. 7. (14 April 2009), pp. 836-845. by Pedro J. Ballester, Paul W. Finn, W. Graham Richards posted to molecule-shapes virtual-screening by massivemayhem on 2009-02-02 14:59:10 as along with 2 people richardbickerton reyez
	CREDO: A Protein-Ligand Interaction Database for Drug Discovery [My Copy] Chemical Biology & Drug Design, Vol. 73, No. 2. (February 2009), pp. 157-167. by Adrian Schreyer, Tom Blundell posted to protein-ligand by massivemayhem on 2009-01-28 11:02:20 as along with 6 people mijam richardbickerton pansapiens bicko nanonan higueruelo
	Properties and Identification of Human Protein Drug Targets. [My Copy] Bioinformatics (Oxford, England) (21 January 2009) by Tala M M. Bakheet, Andrew J J. Doig posted to drug-discovery drug-targets druggability by massivemayhem on 2009-01-28 10:58:49 as along with 2 people sjcockell kshameer
	Fragment-Based de Novo Ligand Design by Multiobjective Evolutionary Optimization [My Copy] J. Chem. Inf. Model. (29 February 2008) by F. Dey, A. Caflisch posted to fragments by massivemayhem on 2009-01-27 16:21:17 as along with 2 people mijogiffin middledomain
	Limitations and lessons in the use of X-ray structural information in drug design [My Copy] Drug Discovery Today, Vol. 13, No. 19-20. (October 2008), pp. 831-841. by A. Davis, S. Stgallay, G. Kleywegt posted to drug-design x-ray by massivemayhem on 2009-01-06 11:22:02 as along with 4 people ramalldf tbinbal pslee thanatos
	AutoPSI: a database for automatic structural classification of protein sequences and structures. [My Copy] Nucleic Acids Res, Vol. 36 (11 October 2007), pp. 398-401. by Fabian Birzele, Jan E. Gewehr, Ralf Zimmer posted to scop by massivemayhem on 2008-10-24 13:17:23 as along with 1 person reyez
	Conformational Sampling of Bioactive Molecules: A Comparative Study [My Copy] J. Chem. Inf. Model. (6 April 2007) by D. K. Agrafiotis, A. C. Gibbs, F. Zhu, S. Izrailev, E. Martin posted to conformers by massivemayhem on 2008-10-08 14:53:32 as along with 3 people apaydin daevans superpyrin
	Discarding Functional Residues from the Substitution Table Improves Predictions of Active Sites within Three-Dimensional Structures [My Copy] PLoS Comput Biol, Vol. 4, No. 10. (3 October 2008), e1000179. by Sungsam Gong, Tom L. Blundell posted to esst by massivemayhem on 2008-10-07 13:08:20 as along with 7 people sebk ssgong gjuggler joseph_x_zhou zwang bicko reyez
	Can we separate active from inactive conformations? [My Copy] Journal of computer-aided molecular design, Vol. 16, No. 2. (February 2002), pp. 105-112. by D. J. Diller, K. M. Merz posted to conformers by massivemayhem on 2008-09-30 16:37:01 as along with 2 people JALumley hryk
	Distinguishing between Bioactive and Modeled Compound Conformations through Mining of Emerging Chemical Patterns [My Copy] J. Chem. Inf. Model., Vol. 48, No. 9. (13 August 2008), pp. 1747-1753. by Jens Auer, Jürgen Bajorath posted to conformers by massivemayhem on 2008-09-30 16:24:09 as along with 3 people JALumley sschurer zimbo1
	Diverse, High-Quality Test Set for the Validation of Protein−Ligand Docking Performance [My Copy] Journal of Medicinal Chemistry, Vol. 50, No. 4. (1 February 2007), pp. 726-741. by Michael J. Hartshorn, Marcel L. Verdonk, Gianni Chessari, et al.Suzanne C. Brewerton, Wijnand T. M. Mooij, Paul N. Mortenson, Christopher W. Murray posted to docking pdb by massivemayhem on 2008-09-25 12:02:39 as along with 9 people flbarroso GermanErlenkamp higueruelo BragilMassoud daevans ramensky hmk superpyrin thanatos
	Concept of Combinatorial De Novo Design of Drug-like Molecules by Particle Swarm Optimization [My Copy] Chemical Biology & Drug Design, Vol. 72, No. 1. (2008), pp. 16-26. by Markus Hartenfeller, Ewgenij Proschak, Andreas Schuller, Gisbert Schneider posted to fragments by massivemayhem on 2008-09-24 14:58:34 as along with 2 people jbesnard reyez
	Deconstructing fragment-based inhibitor discovery. [My Copy] Nature chemical biology, Vol. 2, No. 12. (December 2006), pp. 720-723. by K. Babaoglu, B. K. Shoichet posted to fragments by massivemayhem on 2008-09-24 14:57:42 as along with 1 person pslee
	Chemical Substructures that Enrich for Biological Activity. [My Copy] Bioinformatics (Oxford, England), Vol. 24, No. 21. (11 September 2008), pp. 2518-2525. by Justin Klekota, Frederick P. Roth posted to fragments by massivemayhem on 2008-09-24 11:09:56 as along with 6 people Yanno raiyar zimbo1 dullhunk thanatos higueruelo
	Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit. [My Copy] Chemistry Central journal, Vol. 2 (2008) by N. M. O'Boyle, C. Morley, G. R. Hutchison posted to cheminformatics openbabel pybel by massivemayhem on 2008-07-29 11:49:07 as along with 3 people Scis0000002 ghutchis nicklynch
	Conceptual schema and relational database design (2nd ed.) [My Copy] (1996) by Terry Halpin posted to orm by massivemayhem on 2008-07-22 16:32:14 as along with 1 person nroovers
	MSDmotif: exploring protein sites and motifs [My Copy] BMC Bioinformatics, Vol. 9, No. 1. (2008), 312. by Adel Golovin, Kim Henrick posted to binding-site motifs by massivemayhem on 2008-07-21 11:32:41 as along with 6 people pansapiens HawkinsJohnC tjimenez reyez chad_davis Evangelia
	SuperPred: drug classification and target prediction. [My Copy] Nucleic acids research, Vol. 36, No. Web Server issue. (1 July 2008), pp. 55-59. by M. Dunkel, S. Günther, J. Ahmed, B. Wittig, R. Preissner posted to drug-classification by massivemayhem on 2008-07-17 15:01:44 as along with 2 people pauldobson reyez
	Drugs in sport: a scientist-athlete's perspective: from ambition to neurochemistry [My Copy] Br J Pharmacol, Vol. 154, No. 3. (0000), pp. 496-501. by M. Spedding, C. Spedding posted to journal-club by massivemayhem on 2008-07-17 13:01:24 as
	Pharmacology of anabolic steroids [My Copy] Br J Pharmacol, Vol. 154, No. 3. (0000), pp. 502-521. by A. T. Kicman posted to journal-club by massivemayhem on 2008-07-17 12:54:43 as
	Structure of the catalytic domain of fibroblast collagenase complexed with an inhibitor. [My Copy] Science (New York, N.Y.), Vol. 263, No. 5145. (21 January 1994), pp. 375-377. by B. Lovejoy, A. Cleasby, A. M. Hassell, et al.K. Longley, M. A. Luther, D. Weigl, G. McGeehan, A. B. McElroy, D. Drewry, M. H. Lambert posted to drug-discovery pdb by massivemayhem on 2008-07-01 14:02:40 as along with 1 person mcmathis
	MultiBind and MAPPIS: webservers for multiple alignment of protein 3D-binding sites and their interactions. [My Copy] Nucleic Acids Res, Vol. 36 (8 May 2008), pp. 260-264. by Alexandra Shulman-Peleg, Maxim Shatsky, Ruth Nussinov, Haim J. J. Wolfson posted to binding-site by massivemayhem on 2008-06-11 14:24:40 as along with 2 people higueruelo reyez
	URL decay in MEDLINE - a 4-year follow-up study. [My Copy] Bioinformatics (Oxford, England), Vol. 24, No. 11. (15 April 2008), pp. 1381-1385. by Jonathan D. Wren posted to computer-science by massivemayhem on 2008-06-11 13:32:39 as along with 1 person dullhunk
	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 database protein-ligand by massivemayhem on 2008-06-11 13:27:07 as along with 2 people nickolay blackbart
	Automated analysis of interatomic contacts in proteins. [My Copy] Bioinformatics, Vol. 15, No. 4. (April 1999), pp. 327-332. by V. Sobolev, A. Sorokine, J. Prilusky, E. E. Abola, M. Edelman posted to database protein-ligand by massivemayhem on 2008-06-11 13:17:42 as along with 2 people bicko nickolay
	A searchable database for comparing protein-ligand binding sites for the analysis of structure-function relationships. [My Copy] J Chem Inf Model, Vol. 46, No. 2. (r 2006), pp. 736-742. by N. D. Gold, R. M. Jackson posted to binding-site protein-ligand by massivemayhem on 2008-06-11 13:15:21 as along with 4 people and 1 group medic0747 caporaso blackbart reyez biomedical-nlp
	Structural interaction fingerprint (SIFt): a novel method for analyzing three-dimensional protein-ligand binding interactions. [My Copy] J Med Chem, Vol. 47, No. 2. (15 January 2004), pp. 337-344. by Z. Deng, C. Chuaqui, J. Singh posted to protein-ligand sift by massivemayhem on 2008-06-11 13:13:34 as along with 4 people and 2 groups bio_dataminer ubcg08l apostola sangeetha Bioinformatics insilicodrug
	Relating protein pharmacology by ligand chemistry [My Copy] Nature Biotechnology, Vol. 25, No. 2. (07 February 2007), pp. 197-206. by Michael J. Keiser, Bryan L. Roth, Blaine N. Armbruster, Paul Ernsberger, John J. Irwin, Brian K. Shoichet posted to cheminformatics pharmacology by massivemayhem on 2008-06-10 14:34:56 as along with 7 people ucbcjbm Yanno tjimenez kuhn daevans dgront jerome_ucsf_slb
	CATH--a hierarchic classification of protein domain structures. [My Copy] Structure (London, England : 1993), Vol. 5, No. 8. (15 August 1997), pp. 1093-1108. by C. A. Orengo, A. D. Michie, S. Jones, D. T. Jones, M. B. Swindells, J. M. Thornton posted to protein-classification protein-structure by massivemayhem on 2008-06-10 11:38:52 as along with 14 people and 4 groups ucbcjbm flbarroso kumar_physics semin sebk tjimenez dimka jwm chad_davis Einat caporaso sim82 jteyra gulkur structural_bioinformatics Radiation_Damage Stressosome biomedical-nlp
	PDBcal: a comprehensive dataset for receptor-ligand interactions with three-dimensional structures and binding thermodynamics from isothermal titration calorimetry. [My Copy] Chemical biology & drug design, Vol. 71, No. 6. (June 2008), pp. 529-532. by L. Li, J. J. Dantzer, J. Nowacki, B. J. O'Callaghan, S. O. Meroueh posted to binding-affinity protein-ligand by massivemayhem on 2008-05-22 10:01:46 as along with 3 people flbarroso higueruelo kintoki
	Fast Polygon Area and Newell Normal Computation [My Copy] journal of graphics tools, Vol. 7, No. 2. (2002), pp. 9-13. by Daniel Sunday posted to geometry newell-normal by massivemayhem on 2008-05-20 15:36:14 as

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database	53
snps	48
algorithm	33
protein-ligand	29
reviews	28
networks	27
protein-protein-interactions	23
systems-biology	21
drug-discovery	16
protein-function	16
cancer	13
genetics	13
protein-structure	13
association-studies	12
disease	12
fragments	12
docking	9
binding-site	7
drug-design	7
pathways	7
protein-modelling	7
t1d	7
software	6
virtual-screening	6
binding-affinity	5
bioinformatics	5
chemistry	5
conformers	4
gene-function	4
alignment	3
candidate-genes	3
chemoinformatics	3
crystallography	3
drug-targets	3
evolution	3
genome	3
halogen-bond	3
hydrogen-bonding	3
review	3
small-molecules	3
structural-biology	3
annotation	2
bayesian	2
biological-robustness	2
cell-cycle	2
cheminformatics	2
complexes	2
druggability	2
dynamics	2
esst	2
gene-expression	2
genetic-variation	2
genome-wide	2
human-genome	2
interactome	2
journal-club	2
ligand-shapes	2
mutations	2
p53	2
pdb	2
pharmacophore	2
protein-folding	2
protein-stability	2
sift	2
statistics	2
structure-based	2
water	2
weak-hbonds	2
algorithms	1
blast	1
carbonyl-interactions	1
chemical_biology	1
chemical_libraries	1
chemical_networks	1
clinical	1
clustering	1
cognate-ligand	1
computer-science	1
copy-number-polymorphisms	1
credo	1
cuda	1
desolvation	1
disease-susceptibility	1
drug-classification	1
drug-resistance	1
drugs	1
enrichment-factor	1
epidemiology	1
epigenetics	1
e-science	1
fold-recognition	1
force-field	1
function-prediction	1
genotype	1
geometry	1
gpu	1
graph-theory	1
haplotype	1
hiv	1
homology-modelling	1
imatinib	1
immunology	1
insulin	1
interaction-fingerprints	1
interactions	1
interaction-sites	1
interfaces	1
kd-tree	1
kinases	1
ligand	1
ligand-based-virtual-screening	1
ligand-design	1
ligands	1
lung-cancer	1
medchem	1
medicine	1
metabolites	1
metabolome	1
modularity	1
molecular-dynamics	1
molecular-modelling	1
molecular-recognition	1
molecule-shapes	1
motifs	1
newell-normal	1
nvidia	1
openbabel	1
orm	1
pca	1
pdbbind	1
pharmacology	1
prediction	1
protein	1
protein-classification	1
protein-drug	1
protein-restraints	1
proteomics	1
pybel	1
python	1
quality-assessment	1
recap	1
scop	1
sequence	1
shape-similarity	1
similarity-searching	1
smiles	1
solvent-exposure	1
structural-alignment	1
structural-studies	1
structural-variation	1
synonymous	1
synthetic-lethality	1
text-mining	1
training-data	1
transmembrane	1
visualization	1
x-ray	1

massivemayhem's library 277 articles Export

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