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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)

- 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)

- Andrew S Warren, Ramu Anandakrishnan, Liqing Zhang
- BMC evolutionary biology
- 2010

BACKGROUND
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… (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, 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)

- 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, Zining Zhang, Rory Donovan-Maiye, Daniel M Zuckerman
- Proceedings of the National Academy of Sciences…
- 2016

The ATP synthase (F-ATPase) is a highly complex rotary machine that synthesizes ATP, powered by a proton electrochemical gradient. Why did evolution select such an elaborate mechanism over arguably simpler alternating-access processes that can be reversed to perform ATP synthesis? We studied a systematic enumeration of alternative mechanisms, using… (More)

- Ramu Anandakrishnan, Daniel M Zuckerman
- PloS one
- 2017

ATP-driven proton pumps, which are critical to the operation of a cell, maintain cytosolic and organellar pH levels within a narrow functional range. These pumps employ two very different mechanisms: an elaborate rotary mechanism used by V-ATPase H+ pumps, and a simpler alternating access mechanism used by P-ATPase H+ pumps. Why are two different mechanisms… (More)

The timescales and structure sizes accessible via simulations of atomistic molecular dynamics (MD) can be advanced substantially by two independent techniques: (1) many-core parallelization with graphics processing units (GPUs) and (2) multiscale approximation with hierarchical charge partitioning (HCP). Achieving efficient many-core parallelization on the… (More)