Assistant Professor,
Departments of Computer Science and Physics,
660 McBryde (MC 0106), Virginia Tech
Telephone: 540-231-4237
E-mail @cs.vt.edu : alexey
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 Software |
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Software:
The software below is freely available for non-profit (including academic and educational) use ONLY. To use it for any other purpose, you will need a license: please contact Alexey Onufriev
DSRfit.1.1.beta.math. Example data. The DSR analysis of ligand binding curves. Currently available in the ``Mathematica" language. The code performs the analysis described in two separate publications:
1. Alexey Onufriev, D.A. Case and G. M. Ullmann, `` A Novel View of pH Titration in Biomolecules", Biochemistry, 40, 3413 (2001).
2. Alexey Onufriev and G. M. Ullmann,
``Decomposing Complex Cooperative Ligand Binding into Simple
Components: Connections between Microscopic and Macroscopic models``,
J. Phys. Chem , 108, 11157 (2004)
Macromolecular Contacts Tool. Analysis of residue-residue contacts in biomolecules (proteins, DNA). A GUI-based JAVA (platform free ) code that computes and displays residue-residue contacts for multiple sets of macromolecular snapshots, e.g. coming from various MD trajectories.
Visualization of electrostatic interactions between titratable groups in proteins . Visualization (and analysis) of clusters of electrostatically coupled groups and their interactions in proteins.
J. Myers, G. Grothaus, S. Narayanan, and Alexey Onufriev, ``A simple clustering algorithm can be accurate enough for use in calculations of pK in macromolecules. " (to appear in "Proteins", 2006).
Calculation of pKs using a clustering algorithm .
J. Myers, G. Grothaus, S. Narayanan, and Alexey Onufriev, ``A simple clustering algorithm can be accurate enough for use in calculations of pK in macromolecules. " (to appear in "Proteins", 2006).
Estimation of the effective electrostatic size in the ALPB model .
G. Sigalov, P. Scheffe, and A. Onufriev,
"Incorporating variable dielectric environments into the generalized Born model", J. Chem. Phys., 122, (2005);
G. Sigalov, A. Fenley, and A. Onufriev,
"Analytical Linearized Poisson--Boltzmann Approach: Beyond the Generalized Born
Approximation", J. Chem. Phys., 124, 124902 (2006)
GEM: Computation and Visualization of Electrostaic Potential Around Biomolecules.