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- Ramu Anandakrishnan, Boris Aguilar, Alexey Onufriev
- Nucleic Acids Research
- 2012

The accuracy of atomistic biomolecular modeling and simulation studies depend on the accuracy of the input structures. Preparing these structures for an atomistic modeling task, such as molecular dynamics (MD) simulation, can involve the use of a variety of different tools for: correcting errors, adding missing atoms, filling valences with hydrogens,… (More)

- Boris Aguilar, Ramu Anandakrishnan, Jory Z Ruscio, Alexey V Onufriev
- Biophysical journal
- 2010

This work investigates statistical prevalence and overall physical origins of changes in charge states of receptor proteins upon ligand binding. These changes are explored as a function of the ligand type (small molecule, protein, and nucleic acid), and distance from the binding region. Standard continuum solvent methodology is used to compute, on an equal… (More)

- Ramu Anandakrishnan, Tom R W Scogland, Andrew T Fenley, John C Gordon, Wu-chun Feng, Alexey V Onufriev
- Journal of molecular graphics & modelling
- 2010

Tools that compute and visualize biomolecular electrostatic surface potential have been used extensively for studying biomolecular function. However, determining the surface potential for large biomolecules on a typical desktop computer can take days or longer using currently available tools and methods. Two commonly used techniques to speed-up these types… (More)

- Ramu Anandakrishnan, Alexey Onufriev
- Journal of Computational Chemistry
- 2010

Presented here is a method, the hierarchical charge partitioning (HCP) approximation, for speeding up computation of pairwise electrostatic interactions in biomolecular systems. The approximation is based on multiple levels of natural partitioning of biomolecular structures into a hierarchical set of its constituent structural components. The charge… (More)

- Ramu Anandakrishnan, Charles Baker, Saeed Izadi, Alexey V. Onufriev
- PloS one
- 2013

We propose an approach for approximating electrostatic charge distributions with a small number of point charges to optimally represent the original charge distribution. By construction, the proposed optimal point charge approximation (OPCA) retains many of the useful properties of point multipole expansion, including the same far-field asymptotic behavior… (More)

- Andrew S Warren, Ramu Anandakrishnan, Liqing Zhang
- BMC Evolutionary Biology
- 2009

Characteristics derived from mutation and other mechanisms that are advantageous for survival are often preserved during evolution by natural selection. Some genes are conserved in many organisms because they are responsible for fundamental biological function, others are conserved for their unique functional characteristics. Therefore one would expect the… (More)

- Saeed Izadi, Ramu Anandakrishnan, Alexey V. Onufriev
- The journal of physical chemistry letters
- 2014

Simplified classical water models are currently an indispensable component in practical atomistic simulations. Yet, despite several decades of intense research, these models are still far from perfect. Presented here is an alternative approach to constructing widely used point charge water models. In contrast to the conventional approach, we do not impose… (More)

- Ramu Anandakrishnan, Aleksander Drozdetski, Ross C Walker, Alexey V Onufriev
- Biophysical journal
- 2015

Adequate sampling of conformation space remains challenging in atomistic simulations, especially if the solvent is treated explicitly. Implicit-solvent simulations can speed up conformational sampling significantly. We compare the speed of conformational sampling between two commonly used methods of each class: the explicit-solvent particle mesh Ewald (PME)… (More)

- Ramu Anandakrishnan, Alexey Onufriev
- Journal of Computational Biology
- 2008

In statistical mechanics, the equilibrium properties of a physical system of particles can be calculated as the statistical average over accessible microstates of the system. In general, these calculations are computationally intractable since they involve summations over an exponentially large number of microstates. Clustering algorithms are one of the… (More)

- Ramu Anandakrishnan, Mayank Daga, Alexey V Onufriev
- Journal of chemical theory and computation
- 2011

Molecular dynamics (MD) simulations based on the generalized Born (GB) model of implicit solvation offer a number of important advantages over the traditional explicit solvent based simulations. Yet, in MD simulations, the GB model has not been able to reach its full potential partly due to its computational cost, which scales as ∼n(2), where n is the… (More)