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sobolevnrm's software [143 articles]

Recent papers added to sobolevnrm's library classified by the tag software. You can also see everyone's software.
  • SBML-SAT: a systems biology markup language (SBML) based sensitivity analysis tool
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Zhike Zi, Yanan Zheng, Ann Rundell, Edda Klipp
    posted to systemsbiology software by sobolevnrm on 2008-10-10 12:13:26 as read
  • Very fast prediction and rationalization of p$K_a$ values for protein-ligand complexes
    Proteins: Structure, Function, and Bioinformatics (in press)
    by Delphine C Bas, David M Rogers, Jan H Jensen
    posted to solvation software pka electrostatics bioinformatics by sobolevnrm on 2008-09-03 13:35:31 as read
  • FFTSVD: A Fast Multiscale Boundary-Element Method Solver Suitable for Bio-MEMS and Biomolecule Simulation
    Computer-Aided Design of Integrated Circuits and Systems, IEEE Transactions on, Vol. 25, No. 2. (2006), pp. 274-284.
    by MD Altman, JP Bardhan, B Tidor, JK White
    posted to software mathematics electrostatics by sobolevnrm on 2008-09-03 13:35:31 as read
  • ISIM: A Program for Grand Canonical Monte Carlo Simulations of the Ionic Environment of Biomolecules
    Molecular Simulation, Vol. 30, No. 1. (2004), pp. 45-61.
    by A Vitalis, NA Baker, JA Mccammon
  • notes ISIM: A Program for Grand Canonical Monte Carlo Simulations of the Ionic Environment of Biomolecules
    Molecular Simulation, Vol. 30, No. 1. (2004)
    by A Vitalis, NA Baker, JA Mccammon
  • notes ISIM: A Program for Grand Canonical Monte Carlo Simulations of the Ionic Environment of Biomolecules
    Molecular Simulation, Vol. 30, No. 1. (2004)
    by A Vitalis, NA Baker, JA Mccammon
  • Ontologizer 2.0--a multifunctional tool for GO term enrichment analysis and data exploration
    Bioinformatics, Vol. 24, No. 14. (2008), pp. 1650-1651.
    by Sebastian Bauer, Steffen Grossmann, Martin Vingron, Peter N Robinson
    posted to bioinformatics ontology software by sobolevnrm on 2008-08-28 13:07:41 as read
  • From data to probability densities without histograms
    Computer Physics Communications, Vol. 179, No. 6. (2008)
    by Bernd A Berg, Robert C Harris
    posted to mathematics programming software statistics by sobolevnrm on 2008-08-24 17:18:11 as read
  • MolProbity: all-atom contacts and structure validation for proteins and nucleic acids
    Nucleic Acids Research, Vol. 35, No. suppl_2. (2007)
    by Ian W Davis, Andrew Leaver-Fay, Vincent B Chen, Jeremy N Block, Gary J Kapral, Xueyi Wang, Laura W Murray, Arendall, Jack Snoeyink, Jane S Richardson, David C Richardson
    posted to bioinformatics software structure by sobolevnrm on 2008-08-23 16:23:23 as read
  • Help will be provided for this task: ontology-based annotator web service
    (2008)
    by C Jonquet, Mark A Musen, Nigam H Shah
    posted to bioinformatics ontology software by sobolevnrm on 2008-08-23 16:23:22 as read
  • CHARMMing: A New, Flexible Web Portal for CHARMM
    Journal of Chemical Information and Modeling, No. 1549-9596.
    by Benjamin T Miller, Rishi P Singh, Jeffery B Klauda, Milan Hodošček, Bernard R Brooks, Lee H Woodcock
    posted to moleculardynamics molecularsimulation software by sobolevnrm on 2008-08-18 12:41:34 as read
  • MinActionPath: maximum likelihood trajectory for large-scale structural transitions in a coarse-grained locally harmonic energy landscape
    Nucleic Acids Research, Vol. 35, No. suppl_2. (2007)
    by Joel Franklin, Patrice Koehl, Sebastian Doniach, Marc Delarue
    posted to quasiharmonicmodels software by sobolevnrm on 2008-08-13 21:16:00 as read
  • iTools: A Framework for Classification, Categorization and Integration of Computational Biology Resources
    PLoS ONE, Vol. 3, No. 5. (2008)
    by Ivo D Dinov, Daniel Rubin, William Lorensen, Jonathan Dugan, Jeff Ma, Shawn Murphy, Beth Kirschner, William Bug, Michael Sherman, Aris Floratos, David Kennedy, HV Jagadish, Jeanette Schmidt, Brian Athey, Andrea Califano, Mark Musen, Russ Altman, Ron Kikinis, Isaac Kohane, Scott Delp, Stott D Parker, Arthur W Toga
    posted to bioinformatics software by sobolevnrm on 2008-08-09 22:39:23 as read
  • 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
  • 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 on 2008-07-22 12:39:45 as read along with 1 group baker-group
  • 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
  • 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
  • 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
  • PBEQ-Solver for online visualization of electrostatic potential of biomolecules
    Nucl. Acids Res. (28 May 2008), gkn314.
    by Sunhwan Jo, Miklos Vargyas, Judit Vasko-Szedlar, Benoit Roux, Wonpil Im
    posted to electrostatics software solvation by sobolevnrm on 2008-06-03 13:04:16 as read along with 1 person neils
  • 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
  • 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
  • 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
  • ONTO-PERL: An API supporting the development and analysis of bio-ontologies.
    Bioinformatics (1 February 2008)
  • 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
  • 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
  • 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
  • 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
  • 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.
    posted to pdb2pqr software by sobolevnrm on 2008-04-17 19:28:37 as read along with 1 group baker-group
  • 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
  • GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation
    J. Chem. Theory Comput. (2 February 2008)
  • MScanner: a classifier for retrieving Medline citations
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Graham Poulter, Daniel Rubin, Russ Altman, Cathal Seoighe
  • 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
  • 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
  • A Primer on Python for Life Science Researchers
    PLoS Computational Biology, Vol. 3, No. 11. (1 November 2007), e199.
    by Sebastian Bassi
  • 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
  • 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
  • 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
  • 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
  • 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
  • OBO-Edit - An Ontology Editor for Biologists.
    Bioinformatics (1 June 2007)
    by John Day-Richter, Midori A A Harris, Melissa Haendel, Suzanna Lewis
  • Recent Evolutions of Multiple Sequence Alignment Algorithms
    PLoS Computational Biology, Vol. 3, No. 8. (1 August 2007), e123.
    by Cédric Notredame
  • Visualization software for molecular assemblies
    Current Opinion in Structural Biology, Vol. In Press, Corrected Proof
    by Thomas D Goddard, Thomas E Ferrin
  • Rapid assessment of correlated amino acids from pair-to-pair (P2P) substitution matrices
    Bioinformatics, Vol. 23, No. 14. (2007), pp. 1837-9.
  • Prediction of transition metal-binding sites from apo protein structures
    Proteins (in press)
    by M Babor, S Gerzon, B Raveh, V Sobolev, M Edelman
  • eF-seek: prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape
    Nucleic Acids Research (in press)
  • PI2PE: protein interface/interior prediction engine
    Nucleic Acids Research (in press)
    by H Tjong, S Qin, HX Zhou
  • PMG: online generation of high-quality molecular pictures and storyboarded animations
    Nucleic Acids Research (in press)
    by L Autin, P Tufféry
  • NQ-Flipper: recognition and correction of erroneous asparagine and glutamine side-chain rotamers in protein structures
    Nucleic Acids Research (in press)
    posted to software structure by sobolevnrm on 2007-05-25 14:38:05 as read along with 1 group baker-group
  • 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 pka software solvation by sobolevnrm on 2007-05-25 14:38:05 as read along with 1 group baker-group
  • SwS: a solvation web service for nucleic acids
    Bioinformatics, Vol. 23, No. 8. (2007), pp. 1035-7.
    posted to nucleic_acids software solvation by sobolevnrm on 2007-05-25 14:38:05 as read along with 1 group baker-group
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