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Group: baker-group - with tag software [129 articles]

Neue Artikel von Mitliedern der Gruppe baker-group Gruppe with tag software
  • A meshless, spectrally accurate, integral equation solver for molecular surface electrostatics
    J. Emerg. Technol. Comput. Syst., Vol. 4, No. 2. (April 2008), pp. 1-30.
    by Shih-Hsien Kuo, Bruce Tidor, Jacob White
    posted to electrostatics mathematics software solvation by sobolevnrm to the group baker-group on 2008-07-24 11:45:11 as read
  • Dimensions of knowledge sharing and reuse
    Computers and Biomedical Research, Vol. 25, No. 5. (October 1992), pp. 435-467.
    by Mark A Musen
    posted to bioinformatics ontology software by sobolevnrm to the group baker-group on 2008-07-22 12:39:45 as read
  • Very fast prediction and rationalization of p<I>K</I><SUB><FONT SIZE='-1'>a</FONT></SUB> values for protein-ligand complexes
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2008), NA.
    by Delphine C Bas, David M Rogers, Jan H Jensen
    posted to bioinformatics electrostatics pka software solvation by sobolevnrm to the group baker-group on 2008-07-22 11:48:46 as read along with 1 person RamuAnandakrishnan
  • Visualization of unfavorable interactions in protein folds
    Bioinformatics, Vol. 24, No. 9. (1 May 2008), pp. 1206-1207.
    by Christian X Weichenberger, Piotr Byzia, Manfred J Sippl
    posted to bioinformatics software structure by sobolevnrm to the group baker-group on 2008-06-06 11:24:32 as read
  • HingeMaster: Normal mode hinge prediction approach and integration of complementary predictors
    Proteins (in press)
    by SC Flores, KS Keating, J Painter, F Morcos, K Nguyen, EA Merritt, LA Kuhn, MB Gerstein
    posted to quasiharmonic-models_elastic-network_gnm_nma_pca_etc software by sobolevnrm to the group baker-group on 2008-06-05 11:50:59 as read
  • PROMALS3D: a tool for multiple protein sequence and structure alignments.
    Nucleic Acids Res (20 February 2008)
    by Jimin Pei, Bong-Hyun H Kim, Nick V V Grishin
    posted to bioinformatics software by sobolevnrm to the group baker-group on 2008-05-21 11:38:09 as read along with 2 people newton1234 sunhwan
  • CHARMM-GUI: A web-based graphical user interface for CHARMM
    Journal of Computational Chemistry (in press)
    by S Jo, T Kim, VG Iyer, W Im
    posted to database electrostatics molecular_simulation software by sobolevnrm to the group baker-group on 2008-04-28 11:28:35 as read
  • Analysing the pH-dependent properties of proteins using pKa calculations
    Journal of Molecular Graphics and Modelling, Vol. 25, No. 5. (January 2007), pp. 691-699.
    by Jens E Nielsen
    posted to electrostatics pka software solvation by sobolevnrm to the group baker-group on 2008-04-24 15:00:23 as read
  • ONTO-PERL: An API supporting the development and analysis of bio-ontologies.
    Bioinformatics (1 February 2008)
    by E Antezana, M Egaña, B De Baets, M Kuiper, V Mironov
    posted to bioinformatics ontology software by sobolevnrm to the group baker-group on 2008-04-24 11:35:28 as read along with 4 people dansullivanblk jyuh dullhunk RockHI
  • UCSF Chimera--a visualization system for exploratory research and analysis.
    J Comput Chem, Vol. 25, No. 13. (October 2004), pp. 1605-1612.
    by EF Pettersen, TD Goddard, CC Huang, GS Couch, DM Greenblatt, EC Meng, TE Ferrin
    posted to software visualization by sobolevnrm to the group baker-group on 2008-04-22 12:02:40 as read along with 4 people happy_manatee saunders sjanusz dna
  • Scalable molecular dynamics with NAMD.
    J Comput Chem, Vol. 26, No. 16. (December 2005), pp. 1781-1802.
    by JC Phillips, R Braun, W Wang, J Gumbart, E Tajkhorshid, E Villa, C Chipot, RD Skeel, L Kalé, K Schulten
    posted to molecular_dynamics molecular_simulation software by sobolevnrm to the group baker-group on 2008-04-22 11:48:56 as read along with 10 people and 4 groups vahmurk gisle dimka jwm ttjoseph sangeetha yoel_rf bilab wilsoros ibuch Radiation_Damage Stressosome Bioinformatics insilicodrug
  • Extending the Applicability of the Nonlinear Poisson-Boltzmann Equation: Multiple Dielectric Constants and Multivalent Ions
    J. Phys. Chem. B, Vol. 105, No. 28. (19 July 2001), pp. 6507-6514.
    by W Rocchia, E Alexov, B Honig
    posted to electrostatics software solvation by sobolevnrm to the group baker-group on 2008-04-20 22:33:45 as read along with 1 person onufriev
  • webPIPSA: a web server for the comparison of protein interaction properties
    Nucl. Acids Res. (17 April 2008), gkn181.
    by Stefan Richter, Anne Wenzel, Matthias Stein, Razif R Gabdoulline, Rebecca C Wade
    posted to bioinformatics electrostatics pdb2pqr software structure by sobolevnrm to the group baker-group on 2008-04-18 19:21:27 as ** along with 1 person jyuh
  • A Flexible Grid Framework for Automatic Protein-Ligand Docking
    e-Science and Grid Computing, 2006. e-Science '06. Second IEEE International Conference on (2006), pp. 47-47.
    by D Abramson, C Amoreira, KK Baldridge, L Berstis, C Kondrick, T Peachey
    posted to pdb2pqr software by sobolevnrm to the group baker-group on 2008-04-17 19:28:37 as read
  • WebLogo: A Sequence Logo Generator
    Genome Res., Vol. 14, No. 6. (1 June 2004), pp. 1188-1190.
    by Gavin E Crooks, Gary Hon, John-Marc Chandonia, Steven E Brenner
    posted to bioinformatics software by sobolevnrm to the group baker-group on 2008-03-04 19:56:01 as read along with 4 people and 1 group analogAI indigoviolet xiaobeizhao yevishere EisenLab
  • GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation
    J. Chem. Theory Comput. (2 February 2008)
    by B Hess, C Kutzner, D Vanderspoel, E Lindahl
    posted to molecular_dynamics software by sobolevnrm to the group baker-group on 2008-02-29 12:24:22 as read along with 7 people jwm daevans mmuecke r2s2 middledomain OndrejMarsalek loison
  • MScanner: a classifier for retrieving Medline citations
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Graham Poulter, Daniel Rubin, Russ Altman, Cathal Seoighe
    posted to bioinformatics software by sobolevnrm to the group baker-group on 2008-02-19 19:04:24 as read along with 6 people hpiwowar jyuh Gaetan kharke eveillard bpcusack
  • Prediction of enzyme function based on 3D templates of evolutionarily important amino acids
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by David Kristensen, Matthew R Ward, Andreas M Lisewski, Serkan Erdin, Brian Chen, Viacheslav Fofanov, Marek Kimmel, Lydia Kavraki, Olivier Lichtarge
    posted to bioinformatics software structure by sobolevnrm to the group baker-group on 2008-02-18 12:27:33 as read along with 1 person neils
  • Enhanced performance in prediction of protein active sites with THEMATICS and support vector machines
    Protein Sci, Vol. 17, No. 2. (1 February 2008), pp. 333-341.
    by Wenxu Tong, Ronald J Williams, Ying Wei, Leonel F Murga, Jaeju Ko, Mary J Ondrechen
    posted to bioinformatics database software structure by sobolevnrm to the group baker-group on 2008-01-29 12:28:06 as read
  • A Primer on Python for Life Science Researchers
    PLoS Computational Biology, Vol. 3, No. 11. (1 November 2007), e199.
    by Sebastian Bassi
    posted to misc software by sobolevnrm to the group baker-group on 2008-01-03 12:34:40 as read along with 10 people scryrps giovenko druvus jyuh Ayest dullhunk Ema jfr higueruelo dgroth
  • Automated Builder and Database of Protein/Membrane Complexes for Molecular Dynamics Simulations
    PLoS ONE, Vol. 2, No. 9., e880.
    by S Jo, T Kim, W Im
    posted to biomembranes molecular_dynamics molecular_simulation software by sobolevnrm to the group baker-group on 2007-12-21 12:36:10 as read
  • MOLE: A Voronoi Diagram-Based Explorer of Molecular Channels, Pores, and Tunnels.
    Structure, Vol. 15, No. 11. (13 November 2007), pp. 1357-1363.
    by Martin Petřek, Pavlína Košinová, Jaroslav Koča, Michal Otyepka
    posted to misc molecular_simulation software by sobolevnrm to the group baker-group on 2007-12-12 12:24:26 as read along with 1 person jwm
  • Wordom: a program for efficient analysis of molecular dynamics simulations
    Bioinformatics, Vol. 23, No. 19. (1 October 2007), pp. 2625-2627.
    by Michele Seeber, Marco Cecchini, Francesco Rao, Giovanni Settanni, Amedeo Caflisch
    posted to molecular_simulation software by sobolevnrm to the group baker-group on 2007-11-15 13:15:30 as read along with 6 people and 1 group jyuh barry tmmurali choonpeng hmk LamBras structural_bioinformatics
  • The CHAIN program: forging evolutionary links to underlying mechanisms
    Trends in Biochemical Sciences, Vol. 32, No. 11. (November 2007), pp. 487-493.
    by Andrew F Neuwald
    posted to bioinformatics correlated_mutations software by sobolevnrm to the group baker-group on 2007-11-01 17:28:53 as read
  • HingeProt: Automated prediction of hinges in protein structures
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA.
    by Ugur Emekli, Dina Schneidman-Duhovny, Haim J Wolfson, Ruth Nussinov, Turkan Haliloglu
    posted to structure software quasiharmonic-models_elastic-network_gnm_nma_pca_etc bioinformatics by sobolevnrm to the group baker-group on 2007-09-13 13:14:14 as read along with 3 people barry willpitt higueruelo
  • OBO-Edit - An Ontology Editor for Biologists.
    Bioinformatics (1 June 2007)
    by John Day-Richter, Midori A A Harris, Melissa Haendel, Suzanna Lewis
    posted to software bioinformatics by sobolevnrm to the group baker-group on 2007-09-06 13:21:07 as read along with 8 people yggdrasil leeleong jyuh dullhunk sebastien_vigneau leechuck sgoetz niallhaslam
  • Recent Evolutions of Multiple Sequence Alignment Algorithms
    PLoS Computational Biology, Vol. 3, No. 8. (1 August 2007), e123.
    by Cédric Notredame
    posted to software bioinformatics by sobolevnrm to the group baker-group on 2007-08-31 13:31:38 as read along with 8 people treangen natstreet druvus giovenko agustinarce skhadar hpaces mingzhi
  • Visualization software for molecular assemblies
    Current Opinion in Structural Biology, Vol. In Press, Corrected Proof
    by Thomas D Goddard, Thomas E Ferrin
    posted to visualization software by sobolevnrm to the group baker-group on 2007-08-29 12:24:43 as read along with 4 people BragilMassoud jyuh higueruelo dgront
  • Rapid assessment of correlated amino acids from pair-to-pair (P2P) substitution matrices
    Bioinformatics, Vol. 23, No. 14. (2007), pp. 1837-9.
    by E Eyal, S Pietrokovski, I Bahar
    posted to software correlated_mutations bioinformatics by sobolevnrm to the group baker-group on 2007-08-10 13:06:00 as read
  • Prediction of transition metal-binding sites from apo protein structures
    Proteins (in press)
    by M Babor, S Gerzon, B Raveh, V Sobolev, M Edelman
    posted to structure_prediction software metalloregulation bioinformatics by sobolevnrm to the group baker-group on 2007-08-06 14:33:01 as read
  • eF-seek: prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape
    Nucleic Acids Research (in press)
    by K Kinoshita, Y Murakami, H Nakamura
    posted to software protein-ligand_interactions electrostatics bioinformatics by sobolevnrm to the group baker-group on 2007-06-19 13:29:29 as read
  • PI2PE: protein interface/interior prediction engine
    Nucleic Acids Research (in press)
    by H Tjong, S Qin, HX Zhou
    posted to structure_prediction software bioinformatics by sobolevnrm to the group baker-group on 2007-06-06 13:11:37 as read
  • PMG: online generation of high-quality molecular pictures and storyboarded animations
    Nucleic Acids Research (in press)
    by L Autin, P Tufféry
    posted to visualization structure software misc by sobolevnrm to the group baker-group on 2007-05-25 14:38:05 as read
  • NQ-Flipper: recognition and correction of erroneous asparagine and glutamine side-chain rotamers in protein structures
    Nucleic Acids Research (in press)
    by CX Weichenberger, MJ Sippl
    posted to structure software by sobolevnrm to the group baker-group on 2007-05-25 14:38:05 as read
  • PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations
    Nucleic Acids Research (in press)
    by TJ Dolinsky, P Czodrowski, H Li, JE Nielsen, JH Jensen, G Klebe, NA Baker
    posted to solvation software pka by sobolevnrm to the group baker-group on 2007-05-25 14:38:05 as read
  • SwS: a solvation web service for nucleic acids
    Bioinformatics, Vol. 23, No. 8. (2007), pp. 1035-7.
    by P Auffinger, Y Hashem
    posted to solvation software nucleic_acids by sobolevnrm to the group baker-group on 2007-05-25 14:38:05 as read
  • PROMALS web server for accurate multiple protein sequence alignments
    Nucleic Acids Research (in press)
    by J Pei, BH Kim, M Tang, NV Grishin
    posted to software bioinformatics by sobolevnrm to the group baker-group on 2007-05-25 14:37:08 as read
  • MolProbity: all-atom contacts and structure validation for proteins and nucleic acids
    Nucleic Acids Research (in press)
    by IW Davis, Leaver A Fay, VB Chen, JN Block, GJ Kapral, X Wang, LW Murray, Iii, J Snoeyink, JS Richardson, DC Richardson
    posted to structure software by sobolevnrm to the group baker-group on 2007-05-25 14:37:08 as read
  • The PyMOL Molecular Graphics System
    (2002)
    by WL Delano
    posted to software electrostatics by sobolevnrm to the group baker-group on 2007-05-25 14:36:04 as read
  • A Scientist's Nightmare: Software Problem Leads to Five Retractions
    Science, Vol. 314, No. 5807. (2006), pp. 1856-7.
    by G Miller
    posted to software misc by sobolevnrm to the group baker-group on 2007-05-25 14:36:04 as read
  • Assignment of polar states for protein amino acid residues using a interaction cluster decomposition algorithm and its application to high resolution protein structure modeling
    Proteins, Vol. 66, No. 4. (2007), pp. 824-37.
    by X Li, MP Jacobson, K Zhu, S Zhao, RA Friesner
    posted to software electrostatics by sobolevnrm to the group baker-group on 2007-05-25 14:35:47 as read
  • Stereoselectivity and Expanded Substrate Scope of an Engineered PLP-Dependent Aldolase
    Angewandte Chemie International Edition, Vol. 45, No. 41. (2006), pp. 6824-6.
    by FP Seebeck, A Guainazzi, C Amoreira, KK Baldridge, D Hilvert
    posted to software protein-ligand_interactions electrostatics by sobolevnrm to the group baker-group on 2007-05-25 14:35:46 as read
  • MultiSeq: unifying sequence and structure data for evolutionary analysis
    BMC Bioinformatics, Vol. 7 (2006)
    by E Roberts, J Eargle, D Wright, Luthey Z Schulten
    posted to software bioinformatics by sobolevnrm to the group baker-group on 2007-05-25 14:24:57 as read
  • Scientific Software Development Is Not an Oxymoron
    PLoS Computational Biology, Vol. 2, No. 9. (2006)
    by SM Baxter, SW Day, JS Fetrow, SJ Reisinger
    posted to software career by sobolevnrm to the group baker-group on 2007-05-25 14:23:20 as read
  • CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues
    Nucleic Acids Research, Vol. 34 (2006), pp. W116-W118.
    by J Dundas, Z Ouyang, J Tseng, A Binkowski, Y Turpaz, J Liang
    posted to structure software by sobolevnrm to the group baker-group on 2007-05-25 14:23:17 as read
  • PDB\_Hydro: incorporating dipolar solvents with variable density in the PoissonâBoltzmann treatment of macromolecule electrostatics
    Nucleic Acids Research, Vol. 34 (2006), pp. W38-W42.
    by C Azuara, E Lindahl, P Koehl, H Orland, M Delarue
    posted to solvation software electrostatics by sobolevnrm to the group baker-group on 2007-05-25 14:23:17 as read
  • GROMACS: fast, flexible, and free
    Journal of Computational Chemistry, Vol. 26, No. 16. (2005), pp. 1701-18.
    by D Van der Spoel, E Lindahl, B Hess, G Groenhof, AE Mark, HJC Berendsen
    posted to software molecular_dynamics by sobolevnrm to the group baker-group on 2007-05-25 14:22:45 as read
  • An assessment of the accuracy of methods for predicting hydrogen positions in protein structures
    Proteins, Vol. 61, No. 2. (2005), pp. 296-309.
    by LR Forrest, B Honig
    posted to solvation software electrostatics by sobolevnrm to the group baker-group on 2007-05-25 14:22:45 as read
  • The Backrub Motion: How Protein Backbone Shrugs When a Sidechain Dances
    Structure, Vol. 14 (2006), pp. 265-74.
    by IW Davis, Iii, DC Richardson, JS Richardson
    posted to structure software molecular_dynamics by sobolevnrm to the group baker-group on 2007-05-25 14:19:50 as read
  • The Amber biomolecular simulation programs
    Journal of Computational Chemistry, Vol. 26, No. 16. (2005), pp. 1668-88.
    by DA Case, 3rd, T Darden, H Gohlke, R Luo, Jr, A Onufriev, C Simmerling, B Wang, RJ Woods
    posted to software molecular_dynamics by sobolevnrm to the group baker-group on 2007-05-25 14:18:44 as read
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