GEM (beta.1.0): Computation and Visualization of Electrostaic Potential Around Biomolecules.

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)