Anton 3: twenty microseconds of molecular dynamics simulation before lunch. - Shaw, David E.; Adams, Peter J.; Azaria, Asaph; Bank, Joseph A.; Batson, Brannon; Bell, Alistair; Bergdorf, Michael; Bhatt, Jhanvi; Butts, J. Adam; Correia, Timothy; Dirks, Robert M.; Dror, Ron O.; et al. (2021)

Efficient hyperparameter optimization by way of PAC-Bayes bound minimization. - Cherian, John J.; Taube, Andrew G.; McGibbon, Robert T.; Angelikopoulos, Panagiotis; Blanc, Guy; Snarski, Michael; Richman, Daniel D.; Klepeis, John L.; Shaw, David E. (CoRR, 2020)

Millisecond-scale molecular dynamics simulations on Anton. - Shaw, David E.; Dror, Ron O.; Salmon, John K.; Grossman, J. P.; Mackenzie, Kenneth M.; Bank, Joseph A.; Young, Cliff; Deneroff, Martin M.; Batson, Brannon; Bowers, Kevin J.; Chow, Edmond; Eastwood, Michael P.; et al. (2009)

Millisecond-scale molecular dynamics simulations on Anton. - Shaw, David E.; Dror, Ron O.; Salmon, John K.; Grossman, J. P.; Mackenzie, Kenneth M.; Bank, Joseph A.; Young, Cliff; Deneroff, Martin M.; Batson, Brannon; Bowers, Kevin J.; Chow, Edmond; Eastwood, Michael P.; et al. (2009)

Multiple Minima Problem in Protein Folding: aplhaBB Global Optimization Approach. - Klepeis, John L.; Floudas, Christodoulos A. (2009)

Anton, a special-purpose machine for molecular dynamics simulation. - Shaw, David E.; Deneroff, Martin M.; Dror, Ron O.; Kuskin, Jeffrey; Larson, Richard H.; Salmon, John K.; Young, Cliff; Batson, Brannon; Bowers, Kevin J.; Chao, Jack C.; Eastwood, Michael P.; Gagliardo, Joseph; et al. (Commun. ACM, 2008)

High-throughput pairwise point interactions in Anton, a specialized machine for molecular dynamics simulation. - Larson, Richard H.; Salmon, John K.; Dror, Ron O.; Deneroff, Martin M.; Young, Cliff; Grossman, J. P.; Shan, Yibing; Klepeis, John L.; Shaw, David E. (2008)

A scalable parallel framework for analyzing terascale molecular dynamics simulation trajectories. - Tu, Tiankai; Rendleman, Charles A.; Borhani, David W.; Dror, Ron O.; Gullingsrud, Justin; Jensen, Morten Ø.; Klepeis, John L.; Maragakis, Paul; Miller, Patrick J.; Stafford, Kate A.; Shaw, David E. (2008)

Anton, a special-purpose machine for molecular dynamics simulation. - Shaw, David E.; Deneroff, Martin M.; Dror, Ron O.; Kuskin, Jeffrey; Larson, Richard H.; Salmon, John K.; Young, Cliff; Batson, Brannon; Bowers, Kevin J.; Chao, Jack C.; Eastwood, Michael P.; Gagliardo, Joseph; et al. (2007)

Molecular dynamics - Scalable algorithms for molecular dynamics simulations on commodity clusters. - Bowers, Kevin J.; Chow, Edmond; Xu, Huafeng; Dror, Ron O.; Eastwood, Michael P.; Gregersen, Brent A.; Klepeis, John L.; Kolossváry, István; Moraes, Mark A.; Sacerdoti, Federico D.; Salmon, John K.; Shan, Yibing; et al. (2006)

Analysis and prediction of loop segments in protein structures. - Klepeis, John L.; Floudas, Christodoulos A. (Comput. Chem. Eng., 2005)

Prediction of beta-sheet topology and disulfide bridges in polypeptides. - Klepeis, John L.; Floudas, Christodoulos A. (J. Comput. Chem., 2003)

Ab initio Tertiary Structure Prediction of Proteins. - Klepeis, John L.; Floudas, Christodoulos A. (J. Glob. Optim., 2003)

Ab initio prediction of helical segments in polypeptides. - Klepeis, John L.; Floudas, Christodoulos A. (J. Comput. Chem., 2002)

Comparative study of global minimum energy conformations of hydrated peptides. - Klepeis, John L.; Floudas, Christodoulos A. (J. Comput. Chem., 1999)

Predicting peptide structures using NMR data and deterministic global optimization. - Klepeis, John L.; Floudas, Christodoulos A.; Morikis, Dimitrios; Lambris, John D. (J. Comput. Chem., 1999)

Global optimization approaches in protein folding and peptide docking. - Floudas, Christodoulos A.; Klepeis, John L.; Pardalos, Panos M. (1998)