John L. Klepeis

According to our database, John L. Klepeis authored at least 15 papers between 1998 and 2021.

Collaborative distances:

• Dijkstra number of three.
• Erdős number of three.

2021

Anton 3: twenty microseconds of molecular dynamics simulation before lunch.

David E. Shaw, Peter J. Adams, Asaph Azaria, Joseph A. Bank, Brannon Batson, Alistair Bell, Michael Bergdorf, Jhanvi Bhatt, J. Adam Butts, Timothy Correia, Robert M. Dirks, Ron O. Dror, Michael P. Eastwood, Bruce Edwards, Amos Even, Peter Feldmann, Michael Fenn, Christopher H. Fenton, Anthony Forte, Joseph Gagliardo, Gennette Gill, Maria Gorlatova, Brian Greskamp, J. P. Grossman, Justin Gullingsrud, Anissa Harper, William Hasenplaugh, Mark Heily, Benjamin Colin Heshmat, Jeremy Hunt, Douglas J. Ierardi, Lev Iserovich, Bryan L. Jackson, Nick P. Johnson, Mollie M. Kirk, John L. Klepeis, Jeffrey S. Kuskin, Kenneth M. Mackenzie, Roy J. Mader, Richard McGowen, Adam McLaughlin, Mark A. Moraes, Mohamed H. Nasr, Lawrence J. Nociolo, Lief O'Donnell, Andrew Parker, Jon L. Peticolas, Goran Pocina, Cristian Predescu, Terry Quan, John K. Salmon, Carl Schwink, Keun Sup Shim, Naseer Siddique, Jochen Spengler, Tamas Szalay, Raymond Tabladillo, Reinhard Tartler, Andrew G. Taube, Michael Theobald, Brian Towles, William Vick, Stanley C. Wang, Michael Wazlowski, Madeleine J. Weingarten, John M. Williams, Kevin A. Yuh

Proceedings of the International Conference for High Performance Computing, 2021

2020

Efficient hyperparameter optimization by way of PAC-Bayes bound minimization.

John J. Cherian, Andrew G. Taube, Robert T. McGibbon, Panagiotis Angelikopoulos, Guy Blanc, Michael Snarski, Daniel D. Richman, John L. Klepeis, David E. Shaw

CoRR, 2020

2009

Multiple Minima Problem in Protein Folding: aplhaBB Global Optimization Approach.

John L. Klepeis, Christodoulos A. Floudas

Proceedings of the Encyclopedia of Optimization, Second Edition, 2009

Millisecond-scale molecular dynamics simulations on Anton.

David E. Shaw, Ron O. Dror, John K. Salmon, J. P. Grossman, Kenneth M. Mackenzie, Joseph A. Bank, Cliff Young, Martin M. Deneroff, Brannon Batson, Kevin J. Bowers, Edmond Chow, Michael P. Eastwood, Doug Ierardi, John L. Klepeis, Jeffrey Kuskin, Richard H. Larson, Kresten Lindorff-Larsen, Paul Maragakis, Mark A. Moraes, Stefano Piana, Yibing Shan, Brian Towles

Proceedings of the ACM/IEEE Conference on High Performance Computing, 2009

2008

Anton, a special-purpose machine for molecular dynamics simulation.

David E. Shaw, Martin M. Deneroff, Ron O. Dror, Jeffrey Kuskin, Richard H. Larson, John K. Salmon, Cliff Young, Brannon Batson, Kevin J. Bowers, Jack C. Chao, Michael P. Eastwood, Joseph Gagliardo, J. P. Grossman, C. Richard Ho, Doug Ierardi, István Kolossváry, John L. Klepeis, Timothy Layman, Christine McLeavey, Mark A. Moraes, Rolf Mueller, Edward C. Priest, Yibing Shan, Jochen Spengler, Michael Theobald, Brian Towles, Stanley C. Wang

Commun. ACM, 2008

A scalable parallel framework for analyzing terascale molecular dynamics simulation trajectories.

Tiankai Tu, Charles A. Rendleman, David W. Borhani, Ron O. Dror, Justin Gullingsrud, Morten Ø. Jensen, John L. Klepeis, Paul Maragakis, Patrick J. Miller, Kate A. Stafford, David E. Shaw

Proceedings of the ACM/IEEE Conference on High Performance Computing, 2008

High-throughput pairwise point interactions in Anton, a specialized machine for molecular dynamics simulation.

Richard H. Larson, John K. Salmon, Ron O. Dror, Martin M. Deneroff, Cliff Young, J. P. Grossman, Yibing Shan, John L. Klepeis, David E. Shaw

Proceedings of the 14th International Conference on High-Performance Computer Architecture (HPCA-14 2008), 2008

2006

Molecular dynamics - Scalable algorithms for molecular dynamics simulations on commodity clusters.

Kevin J. Bowers, Edmond Chow, Huafeng Xu, Ron O. Dror, Michael P. Eastwood, Brent A. Gregersen, John L. Klepeis, István Kolossváry, Mark A. Moraes, Federico D. Sacerdoti, John K. Salmon, Yibing Shan, David E. Shaw

Proceedings of the ACM/IEEE SC2006 Conference on High Performance Networking and Computing, 2006

2005

Analysis and prediction of loop segments in protein structures.

John L. Klepeis, Christodoulos A. Floudas

Comput. Chem. Eng., 2005

2003

Ab initio Tertiary Structure Prediction of Proteins.

John L. Klepeis, Christodoulos A. Floudas

J. Glob. Optim., 2003

Prediction of beta-sheet topology and disulfide bridges in polypeptides.

John L. Klepeis, Christodoulos A. Floudas

J. Comput. Chem., 2003

2002

Ab initio prediction of helical segments in polypeptides.

John L. Klepeis, Christodoulos A. Floudas

J. Comput. Chem., 2002

1999

Predicting peptide structures using NMR data and deterministic global optimization.

John L. Klepeis, Christodoulos A. Floudas, Dimitrios Morikis, John D. Lambris

J. Comput. Chem., 1999

Comparative study of global minimum energy conformations of hydrated peptides.

John L. Klepeis, Christodoulos A. Floudas

J. Comput. Chem., 1999

1998

Global optimization approaches in protein folding and peptide docking.

Christodoulos A. Floudas, John L. Klepeis, Panos M. Pardalos

Proceedings of the Mathematical Support for Molecular Biology, 1998