P. Lydia Freddolino
P. Lydia Freddolino
Associate Professor
Verified email at - Homepage
Cited by
Cited by
Accelerating molecular modeling applications with graphics processors
JE Stone, JC Phillips, PL Freddolino, DJ Hardy, LG Trabuco, K Schulten
Journal of computational chemistry 28 (16), 2618-2640, 2007
Molecular dynamics simulations of the complete satellite tobacco mosaic virus
PL Freddolino, AS Arkhipov, SB Larson, A McPherson, K Schulten
Structure 14 (3), 437-449, 2006
COFACTOR: improved protein function prediction by combining structure, sequence and protein–protein interaction information
C Zhang, PL Freddolino, Y Zhang
Nucleic acids research 45 (W1), W291-W299, 2017
Ten-microsecond molecular dynamics simulation of a fast-folding WW domain
PL Freddolino, F Liu, M Gruebele, K Schulten
Biophysical journal 94 (10), L75-L77, 2008
Challenges in protein-folding simulations
PL Freddolino, CB Harrison, Y Liu, K Schulten
Nature physics 6 (10), 751-758, 2010
Prediction of structure and function of G protein-coupled receptors
N Vaidehi, WB Floriano, R Trabanino, SE Hall, P Freddolino, EJ Choi, ...
Proceedings of the National Academy of Sciences 99 (20), 12622-12627, 2002
The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens
N Zhou, Y Jiang, TR Bergquist, AJ Lee, BZ Kacsoh, AW Crocker, ...
Genome biology 20, 1-23, 2019
Coarse grained protein− lipid model with application to lipoprotein particles
AY Shih, A Arkhipov, PL Freddolino, K Schulten
The Journal of Physical Chemistry B 110 (8), 3674-3684, 2006
Stability and dynamics of virus capsids described by coarse-grained modeling
A Arkhipov, PL Freddolino, K Schulten
Structure 14 (12), 1767-1777, 2006
Ab initio protein structure prediction
J Lee, PL Freddolino, Y Zhang
From protein structure to function with bioinformatics, 3-35, 2017
Bacterial adaptation through loss of function
AK Hottes, PL Freddolino, A Khare, ZN Donnell, JC Liu, S Tavazoie
PLoS genetics 9 (7), e1003617, 2013
Force field bias in protein folding simulations
PL Freddolino, S Park, B Roux, K Schulten
Biophysical Journal 96 (9), 3772-3780, 2009
The predicted 3D structure of the human D2 dopamine receptor and the binding site and binding affinities for agonists and antagonists
MYS Kalani, N Vaidehi, SE Hall, RJ Trabanino, PL Freddolino, MA Kalani, ...
Proceedings of the national academy of sciences 101 (11), 3815-3820, 2004
QwikMD—integrative molecular dynamics toolkit for novices and experts
JV Ribeiro, RC Bernardi, T Rudack, JE Stone, JC Phillips, PL Freddolino, ...
Scientific reports 6 (1), 26536, 2016
Common structural transitions in explicit-solvent simulations of villin headpiece folding
PL Freddolino, K Schulten
Biophysical journal 97 (8), 2338-2347, 2009
Assembly of lipoprotein particles revealed by coarse-grained molecular dynamics simulations
AY Shih, PL Freddolino, A Arkhipov, K Schulten
Journal of structural biology 157 (3), 579-592, 2007
Predicted 3D structure for the human β2 adrenergic receptor and its binding site for agonists and antagonists
PL Freddolino, MYS Kalani, N Vaidehi, WB Floriano, SE Hall, ...
Proceedings of the national academy of sciences 101 (9), 2736-2741, 2004
Introducing a spectrum of long-range genomic deletions in human embryonic stem cells using type I CRISPR-Cas
AE Dolan, Z Hou, Y Xiao, MJ Gramelspacher, J Heo, SE Howden, ...
Molecular cell 74 (5), 936-950. e5, 2019
Molecular mechanism of ligand recognition by NR3 subtype glutamate receptors
Y Yao, CB Harrison, PL Freddolino, K Schulten, ML Mayer
The EMBO journal 27 (15), 2158-2170, 2008
Interfacial Activation of Candida antarctica Lipase B: Combined Evidence from Experiment and Simulation
T Zisis, PL Freddolino, P Turunen, MCF van Teeseling, AE Rowan, ...
Biochemistry 54 (38), 5969-5979, 2015
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