Peter L Freddolino is a researcher in the field of biochemistry and genomics. He obtained his B.S. with Honors in Biology from the California Institute of Technology in 2004 and went on to complete his Ph.D. in Biophysics and Computational Biology at the University of Illinois at Urbana-Champaign in 2009.
Freddolino has held several postdoctoral research positions, including at the Tavazoie Lab, Joint Centers for Systems Biology, Columbia University (2011-2014), and the Tavazoie Lab, Lewis-Sigler Institute for Integrative Genomics, Princeton University (2009-2011). He has also been a research fellow and graduate research assistant at the University of Illinois at Urbana-Champaign.
Freddolino's research combines computational and experimental approaches to understand how cells sense and respond to their environment. He utilizes microbial population genetics, systems biology tools, bioinformatic analysis, and molecular and atomistic-level simulations.
Some of his notable publications include:
Freddolino is currently an Assistant Professor of Biological Chemistry, Computational Medicine, and Bioinformatics at the University of Michigan. He is also affiliated with the Department of Biological Chemistry, Department of Computational Medicine and Bioinformatics, Cellular and Molecular Biology Program, and the Center for RNA Biomedicine.
Lydia Freddolino Associate Professor http://freddolino-lab.med.umich.edu/people/lydsf 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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:u5HHmVD_uO8C Cited by: 925
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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:d1gkVwhDpl0C Cited by: 613
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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:isC4tDSrTZIC Cited by: 565
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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:2osOgNQ5qMEC Cited by: 434
Challenges in protein-folding simulations PL Freddolino, CB Harrison, Y Liu, K Schulten Nature physics 6 (10), 751-758, 2010 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:hqOjcs7Dif8C Cited by: 411
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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:u-x6o8ySG0sC Cited by: 375
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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:rO6llkc54NcC Cited by: 364
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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:9yKSN-GCB0IC Cited by: 338
Stability and dynamics of virus capsids described by coarse-grained modeling A Arkhipov, PL Freddolino, K Schulten Structure 14 (12), 1767-1777, 2006 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:IjCSPb-OGe4C Cited by: 330
Ab initio protein structure prediction J Lee, PL Freddolino, Y Zhang From protein structure to function with bioinformatics, 3-35, 2017 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:M3NEmzRMIkIC Cited by: 292
Bacterial adaptation through loss of function AK Hottes, PL Freddolino, A Khare, ZN Donnell, JC Liu, S Tavazoie PLoS genetics 9 (7), e1003617, 2013 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:qUcmZB5y_30C Cited by: 275
Force field bias in protein folding simulations PL Freddolino, S Park, B Roux, K Schulten Biophysical journal 96 (9), 3772-3780, 2009 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:Y0pCki6q_DkC Cited by: 233
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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:UeHWp8X0CEIC Cited by: 206
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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:j3f4tGmQtD8C Cited by: 196
Common structural transitions in explicit-solvent simulations of villin headpiece folding PL Freddolino, K Schulten Biophysical journal 97 (8), 2338-2347, 2009 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:W7OEmFMy1HYC Cited by: 187
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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:zYLM7Y9cAGgC Cited by: 169
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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:SeFeTyx0c_EC Cited by: 166
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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:qjMakFHDy7sC Cited by: 160
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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:LkGwnXOMwfcC Cited by: 151
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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:TQgYirikUcIC Cited by: 149
Lydia Freddolino Associate Professor http://freddolino-lab.med.umich.edu/people/lydsf 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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:u5HHmVD_uO8C Cited by: 925
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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:d1gkVwhDpl0C Cited by: 613
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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:isC4tDSrTZIC Cited by: 565
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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:2osOgNQ5qMEC Cited by: 434
Challenges in protein-folding simulations PL Freddolino, CB Harrison, Y Liu, K Schulten Nature physics 6 (10), 751-758, 2010 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:hqOjcs7Dif8C Cited by: 411
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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:u-x6o8ySG0sC Cited by: 375
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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:rO6llkc54NcC Cited by: 364
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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:9yKSN-GCB0IC Cited by: 338
Stability and dynamics of virus capsids described by coarse-grained modeling A Arkhipov, PL Freddolino, K Schulten Structure 14 (12), 1767-1777, 2006 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:IjCSPb-OGe4C Cited by: 330
Ab initio protein structure prediction J Lee, PL Freddolino, Y Zhang From protein structure to function with bioinformatics, 3-35, 2017 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:M3NEmzRMIkIC Cited by: 292
Bacterial adaptation through loss of function AK Hottes, PL Freddolino, A Khare, ZN Donnell, JC Liu, S Tavazoie PLoS genetics 9 (7), e1003617, 2013 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:qUcmZB5y_30C Cited by: 275
Force field bias in protein folding simulations PL Freddolino, S Park, B Roux, K Schulten Biophysical journal 96 (9), 3772-3780, 2009 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:Y0pCki6q_DkC Cited by: 233
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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:UeHWp8X0CEIC Cited by: 206
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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:j3f4tGmQtD8C Cited by: 196
Common structural transitions in explicit-solvent simulations of villin headpiece folding PL Freddolino, K Schulten Biophysical journal 97 (8), 2338-2347, 2009 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:W7OEmFMy1HYC Cited by: 187
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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:zYLM7Y9cAGgC Cited by: 169
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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:SeFeTyx0c_EC Cited by: 166
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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:qjMakFHDy7sC Cited by: 160
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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:LkGwnXOMwfcC Cited by: 151
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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:TQgYirikUcIC Cited by: 149
Lydia Freddolino Associate Professor http://freddolino-lab.med.umich.edu/people/lydsf 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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:u5HHmVD_uO8C Cited by: 925
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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:d1gkVwhDpl0C Cited by: 613
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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:isC4tDSrTZIC Cited by: 565
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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:2osOgNQ5qMEC Cited by: 434
Challenges in protein-folding simulations PL Freddolino, CB Harrison, Y Liu, K Schulten Nature physics 6 (10), 751-758, 2010 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:hqOjcs7Dif8C Cited by: 411
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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:u-x6o8ySG0sC Cited by: 375
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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:rO6llkc54NcC Cited by: 364
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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:9yKSN-GCB0IC Cited by: 338
Stability and dynamics of virus capsids described by coarse-grained modeling A Arkhipov, PL Freddolino, K Schulten Structure 14 (12), 1767-1777, 2006 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:IjCSPb-OGe4C Cited by: 330
Ab initio protein structure prediction J Lee, PL Freddolino, Y Zhang From protein structure to function with bioinformatics, 3-35, 2017 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:M3NEmzRMIkIC Cited by: 292
Bacterial adaptation through loss of function AK Hottes, PL Freddolino, A Khare, ZN Donnell, JC Liu, S Tavazoie PLoS genetics 9 (7), e1003617, 2013 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:qUcmZB5y_30C Cited by: 275
Force field bias in protein folding simulations PL Freddolino, S Park, B Roux, K Schulten Biophysical journal 96 (9), 3772-3780, 2009 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:Y0pCki6q_DkC Cited by: 233
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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:UeHWp8X0CEIC Cited by: 206
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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:j3f4tGmQtD8C Cited by: 196
Common structural transitions in explicit-solvent simulations of villin headpiece folding PL Freddolino, K Schulten Biophysical journal 97 (8), 2338-2347, 2009 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:W7OEmFMy1HYC Cited by: 187
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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:zYLM7Y9cAGgC Cited by: 169
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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:SeFeTyx0c_EC Cited by: 166
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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:qjMakFHDy7sC Cited by: 160
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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:LkGwnXOMwfcC Cited by: 151
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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:TQgYirikUcIC Cited by: 149
Lydia Freddolino
Associate Professor
http://freddolino-lab.med.umich.edu/people/lydsf
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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:u5HHmVD_uO8C
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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:d1gkVwhDpl0C
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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:isC4tDSrTZIC
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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:2osOgNQ5qMEC
Challenges in protein-folding simulations PL Freddolino, CB Harrison, Y Liu, K Schulten Nature physics 6 (10), 751-758, 2010 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:hqOjcs7Dif8C
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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:u-x6o8ySG0sC
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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:rO6llkc54NcC
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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:9yKSN-GCB0IC
Stability and dynamics of virus capsids described by coarse-grained modeling A Arkhipov, PL Freddolino, K Schulten Structure 14 (12), 1767-1777, 2006 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:IjCSPb-OGe4C
Ab initio protein structure prediction J Lee, PL Freddolino, Y Zhang From protein structure to function with bioinformatics, 3-35, 2017 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:M3NEmzRMIkIC
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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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:UeHWp8X0CEIC
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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:j3f4tGmQtD8C
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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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:SeFeTyx0c_EC
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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:qjMakFHDy7sC
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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:LkGwnXOMwfcC
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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=w2MQZREAAAAJ&citationforview=w2MQZREAAAAJ:TQgYirikUcIC
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