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dgruizs library [99 articles]

Senaste artiklarna i dgruizs bibliotek.
  • MIPS: a database for genomes and protein sequences.
    Nucleic Acids Res, Vol. 30, No. 1. (1 January 2002), pp. 31-34.
    by HW Mewes, D Frishman, U Güldener, 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 3 people and 1 group irenas chad_davis dylanwalker dbk-lab
  • Nuclear Overhauser Effect
    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
    J. Chem. Inf. Model., Vol. 47, No. 1. (22 January 2007), pp. 47-58.
    by A Schuffenhauer, P Ertl, S Roggo, S Wetzel, MA Koch, H Waldmann
    posted to test by dgruiz on 2007-11-21 14:51:48 as ** along with 3 people jerome mdimmic sithmein
  • Protein NMR Spectroscopy: Principles and Practice
    (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.
    Bioinformatics, Vol. 19, No. 17. (22 November 2003), pp. 2308-2310.
    by T Hamelryck, B Manderick
    posted to biopython by dgruiz on 2007-08-23 12:41:31 as ** along with 4 people bicko dgront rabio massivemayhem
  • R: A Language for Data Analysis and Graphics
    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 3 people olympos incovoma xingxu
  • Automatic atom type and bond type perception in molecular mechanical calculations.
    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 4 people and 1 group nigham xdeupi marcvanhouteghem AndreaColetta LabCompMed
  • PRODRG: a tool for high-throughput crystallography of protein–ligand complexes
    Acta Crystallographica Section D: Biological Crystallography, Vol. 60, No. 8. (01 August 2004), pp. 1355-1363.
    by Schüttelkopf, , Van Aalten,
    posted to prodrg by dgruiz on 2007-08-23 10:40:43 as ** along with 1 person simone
  • Docking into knowledge-based potential fields: a comparative evaluation of DrugScore.
    J Med Chem, Vol. 45, No. 10. (9 May 2002), pp. 1967-1970.
    by CA Sotriffer, H Gohlke, G Klebe
    posted to autodock drugscore by dgruiz on 2007-08-22 18:52:18 as ** along with 1 person lillekatt
  • Comparative evaluation of 11 scoring functions for molecular docking.
    J Med Chem, Vol. 46, No. 12. (5 June 2003), pp. 2287-2303.
    by R Wang, Y Lu, S Wang
    posted to autodock docking-general docking-tools-evaluation by dgruiz on 2007-08-22 18:38:05 as ** along with 3 people P2324548 peprovy schlauchi
  • 1H chemical shifts in NMR. Part 18. Ring currents and pi-electron effects in hetero-aromatics
    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.
    J Med Chem, Vol. 47, No. 10. (6 May 2004), pp. 2486-2498.
    by DF Wyss, A Arasappan, MM Senior, YS Wang, BM Beyer, FG Njoroge, MA 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.
    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?
    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.
    Science, Vol. 274, No. 5292. (29 November 1996), pp. 1531-1534.
    by SB Shuker, PJ Hajduk, RP Meadows, SW Fesik
    posted to sar-by-nmr sbdd by dgruiz on 2007-08-21 15:52:18 as ** along with 5 people and 1 group apaydin caporaso cjeans netterpaladin viktor21614 biomedical-nlp
  • A decade of fragment-based drug design: strategic advances and lessons learned
    Nature Reviews Drug Discovery, Vol. 6, No. 3. (09 February 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 3 people bicko massivemayhem jerome_ucsf_slb
  • A relational database for sequence-specific protein NMR data
    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 **
  • Efficient molecular docking of NMR structures: Application to HIV-1 protease
    Protein Sci, Vol. 16, No. 1. (1 January 2007), pp. 43-51.
    by Sheng-You Huang, Xiaoqin Zou
    posted to docking-flexible by dgruiz on 2007-03-19 16:54:08 as ** along with 1 person 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.
    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 8 people and 1 group BragilMassoud radestock lna yongzhao choonpeng weisblum higueruelo nickolay TSRI_MGL
  • The use of chemical shifts and their anisotropies in biomolecular structure determination.
    Curr Opin Struct Biol, Vol. 8, No. 5. (October 1998), pp. 624-630.
    by DA 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.
    Proc Natl Acad Sci U S A, Vol. 95, No. 11. (26 May 1998), pp. 5891-5898.
    by GM Clore, AM 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.
    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.
    J Am Chem Soc, Vol. 128, No. 30. (2 August 2006), pp. 9863-9872.
    by LL Parker, AR Houk, JH Jensen
    posted to cs-prediction hn-cs by dgruiz on 2007-01-18 08:33:50 as **
  • Chemical shifts in proteins come of age
    (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.
    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 3 people BragilMassoud kazemi massivemayhem
  • Pose scoring by NMR.
    J Am Chem Soc, Vol. 126, No. 37. (22 September 2004), pp. 11430-11431.
    by B Wang, K Raha, KM 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.
    J Am Chem Soc, Vol. 127, No. 15. (20 April 2005), pp. 5310-5311.
    by B Wang, KM 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
    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 **
  • Protein-ligand NOE matching: a high-throughput method for binding pose evaluation that does not require protein NMR resonance assignments.
    J Am Chem Soc, Vol. 128, No. 22. (7 June 2006), pp. 7252-7263.
    by KL Constantine, ME Davis, WJ Metzler, L Mueller, BL 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
    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.
    J Am Chem Soc, Vol. 127, No. 22. (8 June 2005), pp. 7978-7979.
    by MA McCoy, MM Senior, DF 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.
    J Comput Chem, Vol. 28, No. 2. (30 January 2007), pp. 612-623.
    by HM Chen, BF Liu, HL Huang, SF Hwang, SY Ho
    posted to pl-docking autodock by dgruiz on 2007-01-09 10:03:56 as ** along with 2 people and 1 group BragilMassoud yongzhao TSRI_MGL
  • Critical assessment of the automated AutoDock as a new docking tool for virtual screening.
    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.
    Protein Sci, Vol. 15, No. 9. (September 2006), pp. 2082-2092.
    by F Cazals, F Proust, RP 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
    J. Med. Chem. (23 September 2006)
    by RA Friesner, RB Murphy, MP Repasky, LL Frye, JR Greenwood, TA Halgren, PC Sanschagrin, DT Mainz
    posted to pl-docking docking-tools-evaluation by dgruiz on 2006-09-27 10:06:37 as ** along with 4 people BragilMassoud daevans LamBras middledomain
  • Hierarchical and multi-resolution representation of protein flexibility.
    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.
    J Med Chem, Vol. 48, No. 2. (27 January 2005), pp. 403-413.
    by MJ Hartshorn, CW Murray, A Cleasby, M Frederickson, IJ Tickle, H Jhoti
    posted to fragment-screening by dgruiz on 2006-09-05 17:09:22 as **
  • Targeting Protein-Protein Interactions with Small Molecules: Challenges and Perspectives for omputational Binding Epitope Detection and Ligand Finding
    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
    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 1 person j3xucite
  • Comparative evaluation of eight docking tools for docking and virtual screening accuracy.
    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 3 people and 2 groups BragilMassoud sangeetha schlauchi Bioinformatics insilicodrug
  • Data clustering: a review
    ACM Comput. Surv., Vol. 31, No. 3. (September 1999), pp. 264-323.
    by AK Jain, MN Murty, PJ Flynn
    posted to review data-mining clustering by dgruiz on 2006-07-07 08:13:10 as ** along with 44 people and 14 groups 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 video_retrieval kdl GroupLens Bioinformatics SRL insilicodrug BioinfoCIPF SGU-CIPF MScResearchRessources NDSiTransitRessources NDS106ProjectRessources NDSIntraVehicularResearch ahat Community_SSTZ
  • Flexible protein-protein docking
    Current Opinion in Structural Biology, Vol. 16, No. 2. (April 2006), pp. 194-200.
    by Alexandre MJJ Bonvin
    posted to haddock pp-docking pp-docking-flexible pp-guided-docking by dgruiz on 2006-07-07 08:12:17 as ** along with 7 people and 3 groups 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.
    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.
    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.
    J Med Chem, Vol. 48, No. 21. (20 October 2005), pp. 6585-6596.
    by IL Alberts, NP Todorov, PM Dean
    posted to docking-flexible by dgruiz on 2005-10-17 12:42:30 as ** along with 5 people and 1 group BragilMassoud apaydin yongzhao kazemi npt11tpn TSRI_MGL
  • Generalized-ensemble algorithms for molecular simulations of biopolymers.
    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
    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 kuhn balicea blackbart ramensky euan junehlee onufriev ashaytan
  • Ligand-induced conformational changes: improved predictions of ligand binding conformations and affinities.
    Biophys J, Vol. 84, No. 4. (April 2003), pp. 2273-2281.
    by TM Frimurer, GH Peters, LF Iversen, HS Andersen, NP Møller, OH Olsen
    posted to flexible-receptor by dgruiz on 2005-07-15 14:06:17 as ** along with 3 people and 1 group yongzhao blackbart kazemi TSRI_MGL
  • Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes.
    J Med Chem, Vol. 46, No. 14. (3 July 2003), pp. 2895-2907.
    by SL McGovern, BK Shoichet
    posted to flexible-receptor by dgruiz on 2005-07-15 14:06:00 as ** along with 2 people tjimenez blackbart
  • Side-chain flexibility in proteins upon ligand binding.
    Proteins, Vol. 39, No. 3. (15 May 2000), pp. 261-268.
    by R Najmanovich, J Kuttner, V Sobolev, M Edelman
    posted to flexible-receptor by dgruiz on 2005-07-15 14:05:37 as ** along with 5 people and 1 group radestock lna yongzhao blackbart LamBras TSRI_MGL
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