Ramu Anandakrishnan
Ramu Anandakrishnan
Edward Via College of Osteopathic Medicine
E-mailová adresa ověřena na: - Domovská stránka
H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations
R Anandakrishnan, B Aguilar, AV Onufriev
Nucleic acids research 40 (W1), W537-W541, 2012
Building water models: a different approach
S Izadi, R Anandakrishnan, AV Onufriev
The journal of physical chemistry letters 5 (21), 3863-3871, 2014
Speed of conformational change: comparing explicit and implicit solvent molecular dynamics simulations
R Anandakrishnan, A Drozdetski, RC Walker, AV Onufriev
Biophysical journal 108 (5), 1153-1164, 2015
Modulation of nucleosomal DNA accessibility via charge-altering post-translational modifications in histone core
AT Fenley, R Anandakrishnan, YH Kidane, AV Onufriev
Epigenetics & chromatin 11, 1-19, 2018
Estimating the number of genetic mutations (hits) required for carcinogenesis based on the distribution of somatic mutations
R Anandakrishnan, RT Varghese, NA Kinney, HR Garner
PLoS computational biology 15 (3), e1006881, 2019
Statistics and physical origins of pK and ionization state changes upon protein-ligand binding
B Aguilar, R Anandakrishnan, JZ Ruscio, AV Onufriev
Biophysical journal 98 (5), 872-880, 2010
Analysis of basic clustering algorithms for numerical estimation of statistical averages in biomolecules
R Anandakrishnan, A Onufriev
Journal of Computational Biology 15 (2), 165-184, 2008
Point charges optimally placed to represent the multipole expansion of charge distributions
R Anandakrishnan, C Baker, S Izadi, AV Onufriev
PloS one 8 (7), e67715, 2013
Why computed protein folding landscapes are sensitive to the water model
R Anandakrishnan, S Izadi, AV Onufriev
Journal of chemical theory and computation 15 (1), 625-636, 2018
Accelerating electrostatic surface potential calculation with multi-scale approximation on graphics processing units
R Anandakrishnan, TRW Scogland, AT Fenley, JC Gordon, W Feng, ...
Journal of Molecular Graphics and Modelling 28 (8), 904-910, 2010
Implicit solvent model for million-atom atomistic simulations: insights into the organization of 30-nm chromatin fiber
S Izadi, R Anandakrishnan, AV Onufriev
Journal of chemical theory and computation 12 (12), 5946-5959, 2016
An N log N approximation based on the natural organization of biomolecules for speeding up the computation of long range interactions
R Anandakrishnan, AV Onufriev
Journal of computational chemistry 31 (4), 691-706, 2010
Differentiating between cancer and normal tissue samples using multi-hit combinations of genetic mutations
S Dash, NA Kinney, RT Varghese, HR Garner, W Feng, ...
Scientific reports 9 (1), 1005, 2019
Biophysical comparison of ATP synthesis mechanisms shows a kinetic advantage for the rotary process
R Anandakrishnan, Z Zhang, R Donovan-Maiye, DM Zuckerman
Proceedings of the National Academy of Sciences 113 (40), 11220-11225, 2016
An n log n Generalized Born Approximation
R Anandakrishnan, M Daga, AV Onufriev
Journal of Chemical Theory and Computation 7 (3), 544-559, 2011
Functional bias in molecular evolution rate of Arabidopsis thaliana
AS Warren, R Anandakrishnan, L Zhang
BMC Evolutionary Biology 10, 1-10, 2010
Identifying multi-hit carcinogenic gene combinations: Scaling up a weighted set cover algorithm using compressed binary matrix representation on a GPU
Q Al Hajri, S Dash, W Feng, HR Garner, R Anandakrishnan
Scientific reports 10 (1), 2022, 2020
CAGm: a repository of germline microsatellite variations in the 1000 genomes project
N Kinney, K Titus-Glover, JD Wren, RT Varghese, P Michalak, H Liao, ...
Nucleic acids research 47 (D1), D39-D45, 2019
ZDHHC3 as a Risk and Mortality Marker for Breast Cancer in African American Women
N Kinney, RT Varghese, R Anandakrishnan, HRS Garner
Cancer informatics 16, 1176935117746644, 2017
Biophysical comparison of ATP-driven proton pumping mechanisms suggests a kinetic advantage for the rotary process depending on coupling ratio
R Anandakrishnan, DM Zuckerman
PloS one 12 (3), e0173500, 2017
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Články 1–20