dgruiz's library 100 articles Export

	The Nuclear Overhauser Effect in Structural and Conformational Analysis, 2nd Edition [My Copy] (10 April 2000) by David Neuhaus, Michael P. Williamson posted to book noe by dgruiz on 2009-02-05 21:36:22 as
	MIPS: a database for genomes and protein sequences. [My Copy] Nucleic acids research, Vol. 30, No. 1. (1 January 2002), pp. 31-34. by H. W. Mewes, D. Frishman, U. Güldener, et al.G. Mannhaupt, K. Mayer, M. Mokrejs, B. Morgenstern, M. Münsterkötter, S. Rudd, B. Weil posted to no-tag by dgruiz on 2008-08-08 14:07:42 as along with 6 people and 1 group cerca lawraga Borelli irenas chad_davis dylanwalker dbk-lab
	Nuclear Overhauser Effect [My Copy] by Joseph H. Noggle, Roger E. Schirmer posted to nmr by dgruiz on 2008-04-27 18:25:31 as
	The Scaffold Tree - Visualization of the Scaffold Universe by Hierarchical Scaffold Classification [My Copy] J. Chem. Inf. Model., Vol. 47, No. 1. (22 January 2007), pp. 47-58. by A. Schuffenhauer, P. Ertl, S. Roggo, S. Wetzel, M. A. Koch, H. Waldmann posted to test by dgruiz on 2007-11-21 14:51:48 as along with 5 people sschurer jerome mdimmic JALumley sithmein
	Protein NMR Spectroscopy: Principles and Practice [My Copy] (17 November 2006) by Cavanagh John posted to nmr by dgruiz on 2007-10-17 11:25:26 as
	PDB file parser and structure class implemented in Python [My Copy] Bioinformatics, Vol. 19, No. 17. (22 November 2003), pp. 2308-2310. by Thomas Hamelryck, Bernard Manderick posted to biopython by dgruiz on 2007-08-23 12:41:31 as along with 7 people and 1 group edws klexa oteri bicko dgront rabio massivemayhem Structural Biology Group TorVergata
	R: A Language for Data Analysis and Graphics [My Copy] Journal of Computational and Graphical Statistics, Vol. 5, No. 3. (1996), pp. 299-314. by Ross Ihaka, Robert Gentleman posted to r by dgruiz on 2007-08-23 12:38:22 as along with 6 people ssgong Inigoleiz eisdur olympos incovoma xingxu
	Automatic atom type and bond type perception in molecular mechanical calculations. [My Copy] J Mol Graph Model (1 February 2006) by Junmei Wang, Wei Wang, Peter A A. Kollman, David A A. Case posted to amber antechamber by dgruiz on 2007-08-23 10:48:28 as along with 5 people and 1 group A_Coletta_Thesis nigham xdeupi marcvanhouteghem AndreaColetta LabCompMed
	PRODRG: a tool for high-throughput crystallography of protein-ligand complexes. [My Copy] Acta crystallographica. Section D, Biological crystallography, Vol. 60, No. Pt 8. (01 August 2004), pp. 1355-1363. by Alexander W. Schüttelkopf, Daan M. van Aalten posted to prodrg by dgruiz on 2007-08-23 10:40:43 as along with 3 people oceanwind jwm simone
	Docking into knowledge-based potential fields: a comparative evaluation of DrugScore. [My Copy] J Med Chem, Vol. 45, No. 10. (9 May 2002), pp. 1967-1970. by C. A. Sotriffer, H. Gohlke, G. Klebe posted to autodock drugscore by dgruiz on 2007-08-22 18:52:18 as along with 2 people AliceWang lillekatt
	Comparative Evaluation of 11 Scoring Functions for Molecular Docking [My Copy] Journal of Medicinal Chemistry, Vol. 46, No. 12. (1 June 2003), pp. 2287-2303. by Renxiao Wang, Yipin Lu, Shaomeng Wang posted to autodock docking-general docking-tools-evaluation by dgruiz on 2007-08-22 18:38:05 as along with 4 people nickolay P2324548 peprovy schlauchi
	1H chemical shifts in NMR. Part 18. Ring currents and pi-electron effects in hetero-aromatics [My Copy] Journal of the Chemical Society, Perkin Transactions 2 (2002), pp. 1081-1091. by Raymond J. Abraham, Matthew Reid posted to parameters ring-currents by dgruiz on 2007-08-22 18:19:55 as
	Non-peptidic small-molecule inhibitors of the single-chain hepatitis C virus NS3 protease/NS4A cofactor complex discovered by structure-based NMR screening. [My Copy] J Med Chem, Vol. 47, No. 10. (6 May 2004), pp. 2486-2498. by D. F. Wyss, A. Arasappan, M. M. Senior, et al.Y. S. Wang, B. M. Beyer, F. G. Njoroge, M. A. McCoy posted to case-history pl-cplx-nmr by dgruiz on 2007-08-22 12:03:53 as
	Biomolecular NMR: a chaperone to drug discovery. [My Copy] Curr Opin Chem Biol, Vol. 10, No. 3. (June 2006), pp. 219-225. by M. Betz, K. Saxena, H. Schwalbe posted to nmr nmr-driven-methods-review pl-cplx-nmr review by dgruiz on 2007-08-21 16:54:19 as
	Ligand-target interactions: what can we learn from NMR? [My Copy] Annu Rev Biophys Biomol Struct, Vol. 34 (2005), pp. 245-266. by T. Carlomagno posted to nmr pl-cplx-nmr review by dgruiz on 2007-08-21 16:53:14 as
	Discovering High-Affinity Ligands for Proteins: SAR by NMR [My Copy] Science, Vol. 274, No. 5292. (29 November 1996), pp. 1531-1534. by Suzanne B. Shuker, Philip J. Hajduk, Robert P. Meadows, Stephen W. Fesik posted to sar-by-nmr sbdd by dgruiz on 2007-08-21 15:52:18 as along with 6 people and 1 group ubcg08l mkrishna apaydin caporaso cjeans viktor21614 biomedical-nlp
	A decade of fragment-based drug design: strategic advances and lessons learned [My Copy] Nat Rev Drug Discov, Vol. 6, No. 3. (09 March 2007), pp. 211-219. by Philip J. Hajduk, Jonathan Greer posted to computer-aided-dd fragment-screening sbdd by dgruiz on 2007-08-21 12:35:14 as along with 6 people and 1 group ubcg08l jerome pslee bicko massivemayhem jerome_ucsf_slb Fragment Based Drug Discovery
	A relational database for sequence-specific protein NMR data [My Copy] Journal of Biomolecular NMR, Vol. 1, No. 3. (1991), pp. 217-236. by Beverly R. Seavey, Elizabeth A. Farr, William M. Westler, John L. Markley posted to bmrb cs-database by dgruiz on 2007-04-20 10:43:42 as along with 1 person kumar_physics
	Efficient molecular docking of NMR structures: application to HIV-1 protease. [My Copy] Protein science : a publication of the Protein Society, Vol. 16, No. 1. (1 January 2007), pp. 43-51. by Sheng-You Y. Huang, Xiaoqin Zou posted to docking-flexible by dgruiz on 2007-03-19 16:54:08 as along with 2 people nickolay hmk
	How Different are Structurally Flexible and Rigid Binding Sites? Sequence and Structural Features Discriminating Proteins that Do and Do not Undergo Conformational Change upon Ligand Binding. [My Copy] J Mol Biol (29 September 2006) by Kannan Gunasekaran, Ruth Nussinov posted to flexibility-descriptor binding-site by dgruiz on 2007-01-18 12:20:56 as along with 10 people and 1 group aqeel reyez BragilMassoud radestock lna yongzhao choonpeng weisblum higueruelo nickolay TSRI_MGL
	The use of chemical shifts and their anisotropies in biomolecular structure determination. [My Copy] Curr Opin Struct Biol, Vol. 8, No. 5. (October 1998), pp. 624-630. by D. A. Case posted to chemical-shifts-proteins p-refinement-by-cs review-cs by dgruiz on 2007-01-18 08:51:42 as
	New methods of structure refinement for macromolecular structure determination by NMR. [My Copy] Proc Natl Acad Sci U S A, Vol. 95, No. 11. (26 May 1998), pp. 5891-5898. by G. M. Clore, A. M. Gronenborn posted to p-refinement-by-cs by dgruiz on 2007-01-18 08:48:19 as
	Simulation of oligopeptide dynamics and folding. The use of NMR chemical shifts to analyse the MD trajectories. [My Copy] J Pept Sci, Vol. 12, No. 1. (January 2006), pp. 33-42. by B. Busetta, P. Picard, G. Précigoux posted to chemical-shifts-proteins cs-prediction ring-currents by dgruiz on 2007-01-18 08:46:24 as
	Cooperative hydrogen bonding effects are key determinants of backbone amide proton chemical shifts in proteins. [My Copy] J Am Chem Soc, Vol. 128, No. 30. (2 August 2006), pp. 9863-9872. by L. L. Parker, A. R. Houk, J. H. Jensen posted to cs-prediction hn-cs by dgruiz on 2007-01-18 08:33:50 as along with 1 person jjurban
	Chemical shifts in proteins come of age [My Copy] (1995), pp. 325-443. by L. Szilagyi posted to chemical-shifts-proteins review by dgruiz on 2007-01-17 19:18:24 as
	Prediction of Protein-Ligand Interactions. Docking and Scoring: Successes and Gaps. [My Copy] J Med Chem, Vol. 49, No. 20. (5 October 2006), pp. 5851-5855. by Andrew R. Leach, Brian K. Shoichet, Catherine E. Peishoff posted to pl-docking docking-review docking-general by dgruiz on 2007-01-17 11:01:11 as along with 4 people ucbcjbm BragilMassoud kazemi massivemayhem
	Pose scoring by NMR. [My Copy] J Am Chem Soc, Vol. 126, No. 37. (22 September 2004), pp. 11430-11431. by B. Wang, K. Raha, K. M. Merz posted to pl-cplx-nmr ligand-csp by dgruiz on 2007-01-15 14:35:53 as
	Validation of the binding site structure of the cellular retinol-binding protein (CRBP) by ligand NMR chemical shift perturbations. [My Copy] J Am Chem Soc, Vol. 127, No. 15. (20 April 2005), pp. 5310-5311. by B. Wang, K. M. Merz posted to pl-cplx-nmr ligand-csp by dgruiz on 2007-01-15 14:34:38 as
	From structure to chemical shift and vice-versa [My Copy] Progress in Nuclear Magnetic Resonance Spectroscopy, Vol. 47, No. 1-2. (31 October 2005), pp. 27-39. by Christopher A. Hunter, Martin J. Packer, Cristiano Zonta posted to review pl-cplx-nmr by dgruiz on 2007-01-15 14:33:05 as along with 1 person yxue
	Protein-ligand NOE matching: a high-throughput method for binding pose evaluation that does not require protein NMR resonance assignments. [My Copy] J Am Chem Soc, Vol. 128, No. 22. (7 June 2006), pp. 7252-7263. by K. L. Constantine, M. E. Davis, W. J. Metzler, L. Mueller, B. L. Claus posted to pl-cplx-nmr ligand-noe by dgruiz on 2007-01-15 14:32:26 as
	Monitoring the Ligand Binding Mode by Proton NMR Chemical Shift Differences [My Copy] ChemMedChem, Vol. 1, No. 11. (2006), pp. 1197-1199. by Srisunder Subramaniam, Stephen l, Allen d posted to pl-cplx-nmr ligand-noe by dgruiz on 2007-01-15 14:28:21 as
	Screening of protein kinases by ATP-STD NMR spectroscopy. [My Copy] J Am Chem Soc, Vol. 127, No. 22. (8 June 2005), pp. 7978-7979. by M. A. McCoy, M. M. Senior, D. F. Wyss posted to std pl-cplx-nmr ligand-noe by dgruiz on 2007-01-15 14:27:19 as
	SODOCK: Swarm optimization for highly flexible protein-ligand docking. [My Copy] J Comput Chem, Vol. 28, No. 2. (30 January 2007), pp. 612-623. by H. M. Chen, B. F. Liu, H. L. Huang, S. F. Hwang, S. Y. Ho posted to pl-docking autodock by dgruiz on 2007-01-09 10:03:56 as along with 4 people and 1 group npt11tpn oteri BragilMassoud yongzhao TSRI_MGL
	Critical assessment of the automated AutoDock as a new docking tool for virtual screening. [My Copy] Proteins (20 September 2006) by Hwangseo Park, Jinuk Lee, Sangyoub Lee posted to autodock docking-tools-evaluation by dgruiz on 2006-09-27 10:15:57 as along with 3 people and 1 group BragilMassoud yongzhao insilico TSRI_MGL
	Revisiting the Voronoi description of protein-protein interfaces. [My Copy] Protein Sci, Vol. 15, No. 9. (September 2006), pp. 2082-2092. by F. Cazals, F. Proust, R. P. Bahadur, J. Janin posted to protein-protein by dgruiz on 2006-09-27 10:15:17 as along with 3 people bicko kdesmond higueruelo
	Extra Precision Glide: Docking and Scoring Incorporating a Model of Hydrophobic Enclosure for Protein-Ligand Complexes [My Copy] J. Med. Chem. (23 September 2006) by R. A. Friesner, R. B. Murphy, M. P. Repasky, et al.L. L. Frye, J. R. Greenwood, T. A. Halgren, P. C. Sanschagrin, D. T. Mainz posted to pl-docking docking-tools-evaluation by dgruiz on 2006-09-27 10:06:37 as along with 6 people snichols15 flbarroso BragilMassoud daevans LamBras middledomain
	Hierarchical and multi-resolution representation of protein flexibility. [My Copy] Bioinformatics (18 September 2006) by Yong Zhao, Daniel Stoffler, Michel Sanner posted to flexible-receptor by dgruiz on 2006-09-23 12:26:19 as along with 4 people and 1 group BragilMassoud yongzhao kazemi LamBras TSRI_MGL
	Fragment-Based Lead Discovery Using X-ray Crystallography [My Copy] Journal of Medicinal Chemistry, Vol. 48, No. 2. (1 January 2005), pp. 403-413. by Michael J. Hartshorn, Christopher W. Murray, Anne Cleasby, Martyn Frederickson, Ian J. Tickle, Harren Jhoti posted to fragment-screening by dgruiz on 2006-09-05 17:09:22 as along with 2 people and 1 group ubcg08l pslee Fragment Based Drug Discovery
	Targeting Protein-Protein Interactions with Small Molecules: Challenges and Perspectives for omputational Binding Epitope Detection and Ligand Finding [My Copy] Current Medicinal Chemistry, Vol. 13, No. 22. (September 2006), pp. 2607-2625. by Gonzalez-Ruiz, Domingo, Gohlke, Holger posted to protein-protein-interactions by dgruiz on 2006-09-01 07:18:21 as along with 2 people aqeel higueruelo
	Accurate prediction of protein torsion angles using chemical shifts and sequence homology [My Copy] Magnetic Resonance in Chemistry, Vol. 44, No. S1. (2006), pp. S158-S167. by Stephen Neal, Mark Berjanskii, Haiyan Zhang, David S. Wishart posted to p-refinement-by-cs by dgruiz on 2006-08-16 13:21:37 as along with 3 people apaydin babakap j3xucite
	Comparative evaluation of eight docking tools for docking and virtual screening accuracy. [My Copy] Proteins, Vol. 57, No. 2. (1 November 2004), pp. 225-242. by E. Kellenberger, J. Rodrigo, P. Muller, D. Rognan posted to docking-tools-evaluation by dgruiz on 2006-07-07 08:17:21 as along with 5 people and 2 groups klexa oteri BragilMassoud sangeetha schlauchi Bioinformatics insilicodrug
	Data clustering: a review [My Copy] ACM Comput. Surv., Vol. 31, No. 3. (September 1999), pp. 264-323. by A. K. Jain, M. N. Murty, P. J. Flynn posted to review data-mining clustering by dgruiz on 2006-07-07 08:13:10 as along with 62 people and 15 groups emailhy erikv thegoose urvoy stharward thefillm operon avoregnitiv fer votis pick600 pbk nhoussos qwermish svozil takeha-e eabait mthomure mercutio egh ericyu karbak pdlug thsant mapio mhay davidbrooks imouthesmp dfrankow rahul marcius stagediver sterovetta sangeetha chadhogg sdvillal dgront styliani alexhofmann gane5h ianturton bigbossman perceptron allmensch aviad_work julianpan atbrew sugarexpletive KillianKay mkolar sajan dvisoin theodora jcsilva furykerry koles paulovn AbnerCYH tnhh flaviovdf dragonrez iraklis elan video_retrieval kdl GroupLens Bioinformatics SRL insilicodrug BioinfoCIPF SGU-CIPF MScResearchRessources NDSiTransitRessources NDS106ProjectRessources NDSIntraVehicularResearch ahat Community_SSTZ
	Flexible protein-protein docking [My Copy] Current Opinion in Structural Biology In Theory and simulation/Macromolecular assemblages - Joel Janin and Michael Levitt/Edward H Egelman and Andrew GW Leslie, Vol. 16, No. 2. (April 2006), pp. 194-200. by Alexandre M. J. J. Bonvin posted to haddock pp-docking pp-docking-flexible pp-guided-docking by dgruiz on 2006-07-07 08:12:17 as along with 11 people and 3 groups timg flbarroso oteri laurabailey aqeel bicko yongzhao ima sangeetha gloria higueruelo Bioinformatics TSRI_MGL insilicodrug
	Constrained refinement based on NOE and chemical shift information: the monomer form of arginine-vasopressin-like insect factor. [My Copy] J Pept Sci, Vol. 3, No. 2. (r 1997), pp. 133-140. by B. Busetta, P. Picard posted to p-refinement-by-cs by dgruiz on 2006-02-03 12:03:21 as
	Representativity of target families in the Protein Data Bank: impact for family-directed structure-based drug discovery. [My Copy] Drug Discov Today, Vol. 10, No. 23-24. (December 2005), pp. 1629-1637. by J. Mestres posted to docking-general by dgruiz on 2006-01-04 12:59:07 as
	Receptor flexibility in de novo ligand design and docking. [My Copy] J Med Chem, Vol. 48, No. 21. (20 October 2005), pp. 6585-6596. by I. L. Alberts, N. P. Todorov, P. M. Dean posted to docking-flexible by dgruiz on 2005-10-17 12:42:30 as along with 4 people and 1 group BragilMassoud apaydin yongzhao kazemi TSRI_MGL
	Generalized-ensemble algorithms for molecular simulations of biopolymers. [My Copy] Biopolymers, Vol. 60, No. 2. (2001), pp. 96-123. by A. Mitsutake, Y. Sugita, Y. Okamoto posted to molecular-dynamics by dgruiz on 2005-08-22 16:43:38 as along with 3 people baaden shuns andreasauerwein
	The Many Roles of Computation in Drug Discovery [My Copy] Science, Vol. 303, No. 5665. (19 March 2004), pp. 1813-1818. by William L. Jorgensen posted to computer-aided-dd by dgruiz on 2005-08-21 18:33:03 as along with 8 people snichols15 kuhn balicea blackbart ramensky euan onufriev ashaytan
	Ligand-induced conformational changes: improved predictions of ligand binding conformations and affinities. [My Copy] Biophys J, Vol. 84, No. 4. (April 2003), pp. 2273-2281. by T. M. Frimurer, G. H. Peters, L. F. Iversen, H. S. Andersen, N. P. Møller, O. H. Olsen posted to flexible-receptor by dgruiz on 2005-07-15 14:06:17 as along with 4 people and 1 group oteri yongzhao blackbart kazemi TSRI_MGL
	Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes. [My Copy] J Med Chem, Vol. 46, No. 14. (3 July 2003), pp. 2895-2907. by S. L. McGovern, B. K. Shoichet posted to flexible-receptor by dgruiz on 2005-07-15 14:06:00 as along with 2 people tjimenez blackbart

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pl-cplx-nmr	16
flexible-receptor	13
pl-docking	13
review	10
docking-flexible	7
ligand-noe	7
autodock	6
cs-prediction	6
docking-tools-evaluation	6
pp-docking	6
pp-guided-docking	6
binding-site	5
genetic-algorithm	5
nmr	5
protein-csp	5
chemical-shifts-proteins	4
docking-general	4
p-refinement-by-cs	4
docking-review	3
haddock	3
pl-guided-docking	3
case-history	2
computer-aided-dd	2
cs-database	2
docking-dataset	2
fragment-screening	2
ligand-csp	2
molecular-dynamics	2
nmr-driven-methods-review	2
ppi	2
ppim	2
prodrg	2
protein-protein	2
ring-currents	2
sar-by-nmr	2
sbdd	2
shifts	2
amber	1
antechamber	1
biopython	1
bmrb	1
book	1
clustering	1
data-mining	1
diagnostic-cs	1
drugscore	1
flexibility-descriptor	1
hn-cs	1
ism	1
kinases	1
ligand-preparation	1
noe	1
parameters	1
pp-cplx-nmr	1
pp-docking-flexible	1
protein-protein-interactions	1
r	1
restrained-docking	1
review-cs	1
review-docking	1
std	1
test	1

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