Preprints

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2008

Krisnan and Bhatia, "SOAs for Scientific Applications: Experiences and Challenges", 2008 IEEE e-Science Conference, Bangalore, India

2007

Ding et al, "Customized Plug-in Modules for Community Scheduler Framework (CSF4) for Life Sciences Applications", New Generation Computing Special Issue on Life Sciences Grid, In Press

Cheng et al, "Finite Element Analysis of the Time-Dependen Smoluchowski Equation for Acetylcholinesterase Reaction Rate Calculations", Biophysical Journal, Accepted

Amaro et al, "Remarkable Loop Flexibility in Avian Influenza N1 and Its Implications for Antiviral Drug Design", JACS, In Press

Yu et al, "Feature-Preserving Adative Mesh Generation for Molecular Modeling", PLoS Computational Biology, Submitted.

Dolinsky et al, "PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations", NAR Web server Issue

Chang et al, "Binding Pathways of Ligands to HIV-1 Protease: Coarse-grained and Atomistic Simulations", Chem Biol Drug Des

Cheng et al, "Acetylcholinesterase: Mechanisms of Covalent Inhibition of Wild-Type and H447I Mutant Determined by Computational Analyses", JACS, 2007

Cheng et al, "Continuum simulations of acetylcholine diffusion with reaction-determined boundaries in neuromuscular junction models", Biophysical Journal, 2007

Zhao and Sanner, FLIPDock: Docking flexible ligands into flexible receptors, Proteins, 2007

Amaro et al, "Avian Flu Grid: International Collaborative Environment for Team Science on Avian Influenza", Poster at PRAGMA 13, NCSA, IL

Krishnan et al, "Opal -- Enabling the Web 2.0 paradigm for biomedical and metagenomcis applications", Poster at PRAGMA 13, NCSA, IL

Grant et al, "Multivariate Analysis of Conserved Sequence–Structure Relationships in Kinesins: Coupling of the Active Site and a Tubulin-binding Sub-domain", JMB, 2007

Clementi et al, "Providing Dynamic Virtualized Access to Grid Resources via the Web 2.0 Paradigm", GCE07, 2007

Yong and Sanner, "Protein-ligand docking with multiple flexible side chains", J Comput Aided Mol Des, 2007

2006

Perryman et al on "Restrained MD of HIV protease", Biopolymers, Feb 2006

Dzubiella et al on "Continuum Solvent Models", Physics Review Letters, March 2006

Abramson et al, CCGrid Conference on "Application Deployment in PRAGMA Testbed", Proceedings of CCGrid, May 2006

Bailey et al, NAR on "MEME Web Server", In Press

Kaiser et al, PDPTA on "MYMPI & Python MPI Programming", In Press

Krishnan et al, ICWS on "Opal web service wrapper", In Press

Li et al, CCGrid/BioGrid Workshop on "Cyberinfrastructure for bioinformatics", Proceedings of CCGrid, May 2006

Perryman et al on "Relaxed Complex Method and HIV-1 Protease Drug Design", Chemical Biology & Drug Design, May 2006

Li et al, NCRR Annual Meeting on "Cyberinfrastructure for Multiscale Modeling in Biomedical Research", Poster, June 2006

Baitaluk et al, NAR on "BiologicalNetworks Web Server", Open Access, July 2006

Falim et al, "Contributions of sustained INa and IKv43 to transmural heterogeneity of early repolarization and arrhythmogenesis in canine left ventricular myocytes", Am J Physiol Heart Circ Physiol 291: H2617–H2629, 2006

Constandi et al, on "Diastolic properties in transition to failure in mouse model of dilatation", American J Physiology & Heart Circulation Physiology, July 2006

Li et al, CTWatch Quarterly on "Cyberinfrastructure for Multiscale Modeling in Biomedical Research", CTwatch Quarterly, Aug 2006.

Saucerman et al, on "PKA mediated phosphorylation gradient in live cardiac myocytes", PNAS, Aug 2006.

Ding et al, GCE'06 on "My WorkSphere", In Press

Hunter et al, "Multiscale Modeling: Physiome Project Standards, Tools and Databases", Computer, Nov 2006

2005

Mueller et al, "GAMA", IEEE International Conf e-Science and Grid Computing

Batailuc et al, "PathSys database", BMC Bioinformatics

2004

Song et al, "Finite Element Solution of Steady-state Smoluchowski Equation for Rate Constant Calculations, Biophysical Journal

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