| 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 | 927 | 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 | 621 | 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 | 584 | 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 | 436 | 2008 |
| Challenges in protein-folding simulations PL Freddolino, CB Harrison, Y Liu, K Schulten Nature physics 6 (10), 751-758, 2010 | 415 | 2010 |
| 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 | 388 | 2019 |
| 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 | 377 | 2002 |
| 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 | 341 | 2006 |
| Stability and dynamics of virus capsids described by coarse-grained modeling A Arkhipov, PL Freddolino, K Schulten Structure 14 (12), 1767-1777, 2006 | 334 | 2006 |
| Ab initio protein structure prediction J Lee, PL Freddolino, Y Zhang From protein structure to function with bioinformatics, 3-35, 2017 | 298 | 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 | 276 | 2013 |
| Force field bias in protein folding simulations PL Freddolino, S Park, B Roux, K Schulten Biophysical journal 96 (9), 3772-3780, 2009 | 234 | 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 | 207 | 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 | 201 | 2016 |
| Common structural transitions in explicit-solvent simulations of villin headpiece folding PL Freddolino, K Schulten Biophysical journal 97 (8), 2338-2347, 2009 | 188 | 2009 |
| 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 | 172 | 2019 |
| 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 | 169 | 2007 |
| 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 | 160 | 2015 |
| 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 | 160 | 2004 |
| 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 | 153 | 2008 |
