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2020 – today
- 2021
[c8]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:
Anton 3: twenty microseconds of molecular dynamics simulation before lunch. SC 2021: 1- 2020
- [i1]John J. Cherian, Andrew G. Taube, Robert T. McGibbon, Panagiotis Angelikopoulos, Guy Blanc, Michael Snarski, Daniel D. Richman, John L. Klepeis, David E. Shaw:
Efficient hyperparameter optimization by way of PAC-Bayes bound minimization. CoRR abs/2008.06431 (2020)
2000 – 2009
- 2009
- [c7]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:
Millisecond-scale molecular dynamics simulations on Anton. SC 2009 - [c6]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:
Millisecond-scale molecular dynamics simulations on Anton. SC 2009 - [r1]John L. Klepeis, Christodoulos A. Floudas:
Multiple Minima Problem in Protein Folding: aplhaBB Global Optimization Approach. Encyclopedia of Optimization 2009: 2490-2497 - 2008
- [j7]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:
Anton, a special-purpose machine for molecular dynamics simulation. Commun. ACM 51(7): 91-97 (2008) - [c5]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:
High-throughput pairwise point interactions in Anton, a specialized machine for molecular dynamics simulation. HPCA 2008: 331-342 - [c4]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:
A scalable parallel framework for analyzing terascale molecular dynamics simulation trajectories. SC 2008: 56 - 2007
- [c3]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:
Anton, a special-purpose machine for molecular dynamics simulation. ISCA 2007: 1-12 - 2006
- [c2]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:
Molecular dynamics - Scalable algorithms for molecular dynamics simulations on commodity clusters. SC 2006: 84 - 2005
- [j6]John L. Klepeis, Christodoulos A. Floudas:
Analysis and prediction of loop segments in protein structures. Comput. Chem. Eng. 29(3): 423-436 (2005) - 2003
- [j5]John L. Klepeis, Christodoulos A. Floudas:
Prediction of beta-sheet topology and disulfide bridges in polypeptides. J. Comput. Chem. 24(2): 191-208 (2003) - [j4]John L. Klepeis, Christodoulos A. Floudas:
Ab initio Tertiary Structure Prediction of Proteins. J. Glob. Optim. 25(1): 113-140 (2003) - 2002
- [j3]John L. Klepeis, Christodoulos A. Floudas:
Ab initio prediction of helical segments in polypeptides. J. Comput. Chem. 23(2): 245-266 (2002)
1990 – 1999
- 1999
- [j2]John L. Klepeis, Christodoulos A. Floudas:
Comparative study of global minimum energy conformations of hydrated peptides. J. Comput. Chem. 20(6): 636-654 (1999) - [j1]John L. Klepeis, Christodoulos A. Floudas, Dimitrios Morikis, John D. Lambris:
Predicting peptide structures using NMR data and deterministic global optimization. J. Comput. Chem. 20(13): 1354-1370 (1999) - 1998
- [c1]Christodoulos A. Floudas, John L. Klepeis, Panos M. Pardalos:
Global optimization approaches in protein folding and peptide docking. Mathematical Support for Molecular Biology 1998: 141-171
Coauthor Index
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