Onufriev Lab

Software

Recent packages can also be found at https://github.com/Onufriev-Lab

DROSOPHILA INTERPHASE NUCLEUS at TAD resolution.

Details: "Strong interactions between highly dynamic lamina-associated domains and the nuclear envelope stabilize the 3D architecture of Drosophila interphase chromatin ", by Tolokh et al. (2023).

AASC: Analytical Surface Charge and Electric Field around molecules.

Details: "A closed-form, analytical approximation for apparent surface charge and electric field of molecules", Dan Folescu and Alexey V. Onufriev, (2022).

GBMC: A Monte-Carlo code and parameter files to perform implcit solvent/explcit ions calculations.

Details: "Explicit ions/implicit water generalized Born model for nucleic acids", Igor S. Tolokh, Dennis G. Thomas, and Alexey V. Onufriev, JCP 148, 195101 (2018).

Relaxed, atomistic structure of a 30nm chromatin fiber (40 nuncleosomes).

Along with amber format topology and coordinate files for (multiresolution, HCP) MD simulation in implicit solvent.

Details are in "Implicit Solvent Simulation of Million-Atom Structures: Insights into the Organization of 30-nm Chromatin Fiber" by Saeed Izadi, Ramu Anandakrishnan, and Alexey V. Onufriev, JCTC, (2016).

H++: Automated prediction of pK and protonation states in macromolecules.

The web server computes pK values of ionizable groups in macromolecules and adds missing hydrogen atoms according to the specified pH of the environment. Given a (PDB) structure file on input, H++ outputs the completed structure in several common formats (PDB, PQR, AMBER inpcrd/prmtop) and provides a set of tools for analysis of electrostatic-related molecular properties.

Details: Anandakrishnan R, Aguilar B, Onufriev AV. ``H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations.", Nucleic Acids Res. 40, W537-41 (2012).

12CG. Coarse-grained Molecular Dynamics of the DNA.

This is a set of programs to perform coarse-grained MD simulations and calculations of the DNA heat conductivity described in Alexander V. Savin, Mikhail A. Mazo, Irina P. Kikot, Leonid I. Manevitch, and Alexey V. Onufriev. ``Heat conductivity of the DNA double helix", Phys. Rev. B 83, 245406 (2011)

GBNSR6 (2.0, MSMS-based): Generalized Born and Charge Asymmetric Generalized Born solvation energies of molecules based on the R6 effective Born radii.

Boris Aguilar, Richard Shadrach, and Alexey V. Onufriev. ``Reducing the Secondary Structure Bias in the Generalized Born Model via R6 Effective Radii", J. Chem. Theory and Comput., 6, 3613–3630 (2010).

Mukhopadhyay et al. "Introducing Charge Hydration Asymmetry into the Generalized Born Model"

GEM (1.3): Computation and Visualization of Electrostatic Potential Around Biomolecules.

John C. Gordon, Andrew T. Fenley, and A. Onufriev, ``An Analytical Approach to Computing Biomolecular Electrostatic Potential, II: Validation and Applications", Journal of Chemical Physics, 129, 075102 (2008)

PATHFINDER (beta 0.1): analysis of voids in macromolecules.

Jory Z. Ruscio, Deept Kumar, Maulik Shukla, Michael G. Prisant, T. M. Murali, and Alexey V. Onufriev, ``Atomic level computational identification of ligand migration pathways between solvent and binding site in myoglobin", Proceedings of the National Academy of Sciences, (USA), 15, 9204-9209 (2008).

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 some analysis) of clusters of electrostatically coupled groups and their interactions in proteins. A simple rasmol-based script.

Myers J, Grothaus G, Narayanan S, Onufriev A, "A simple clustering algorithm can be accurate enough for use in calculations of pKs in macromolecules", Proteins, 63, 928-938 (2006).

Calculation of pKs using a clustering algorithm.

Myers J, Grothaus G, Narayanan S, Onufriev A, "A simple clustering algorithm can be accurate enough for use in calculations of pKs in macromolecules", Proteins, 63, 928-938 (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)

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)