John L. Klepeis

17 papers A* 2A 5Journal 8Unranked 1

Year	Rank	Type	Title / Venue / Authors
2021	A	`conf`	Anton 3: twenty microseconds of molecular dynamics simulation before lunch. SC 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
2020	J	`jnl`	Efficient hyperparameter optimization by way of PAC-Bayes bound minimization. CoRR John J. Cherian, Andrew G. Taube, Robert T. McGibbon, Panagiotis Angelikopoulos, Guy Blanc, Michael Snarski, Daniel D. Richman, John L. Klepeis, David E. Shaw
2009	A	`conf`	Millisecond-scale molecular dynamics simulations on Anton. SC 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
2009	A	`conf`	Millisecond-scale molecular dynamics simulations on Anton. SC 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
2009	—	`ch.`	Multiple Minima Problem in Protein Folding: aplhaBB Global Optimization Approach. Encyclopedia of Optimization John L. Klepeis, Christodoulos A. Floudas
2008	A	`conf`	A scalable parallel framework for analyzing terascale molecular dynamics simulation trajectories. SC 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
2008	J	`jnl`	Anton, a special-purpose machine for molecular dynamics simulation. Commun. ACM 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
2008	A*	`conf`	High-throughput pairwise point interactions in Anton, a specialized machine for molecular dynamics simulation. HPCA 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
2007	A*	`conf`	Anton, a special-purpose machine for molecular dynamics simulation. ISCA 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
2006	A	`conf`	Molecular dynamics - Scalable algorithms for molecular dynamics simulations on commodity clusters. SC 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
2005	J	`jnl`	Analysis and prediction of loop segments in protein structures. Comput. Chem. Eng. John L. Klepeis, Christodoulos A. Floudas
2003	J	`jnl`	Ab initio Tertiary Structure Prediction of Proteins. J. Glob. Optim. John L. Klepeis, Christodoulos A. Floudas
2003	J	`jnl`	Prediction of beta-sheet topology and disulfide bridges in polypeptides. J. Comput. Chem. John L. Klepeis, Christodoulos A. Floudas
2002	J	`jnl`	Ab initio prediction of helical segments in polypeptides. J. Comput. Chem. John L. Klepeis, Christodoulos A. Floudas
1999	J	`jnl`	Comparative study of global minimum energy conformations of hydrated peptides. J. Comput. Chem. John L. Klepeis, Christodoulos A. Floudas
1999	J	`jnl`	Predicting peptide structures using NMR data and deterministic global optimization. J. Comput. Chem. John L. Klepeis, Christodoulos A. Floudas, Dimitrios Morikis, John D. Lambris
1998	—	`conf`	Global optimization approaches in protein folding and peptide docking. Mathematical Support for Molecular Biology Christodoulos A. Floudas, John L. Klepeis, Panos M. Pardalos