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Ultra-fast Evaluation of Protein Energies Directly from Sequence

Gevorg Grigoryan, Fei Zhou, Steve R Lustig, Gerbrand Ceder, Dane Morgan, Amy E. Keating
2005 PLoS Computational Biology  
Citation: Grigoryan G, Zhou F, Lustig SR, Ceder G, Morgan D, et al. (2006) Ultra-fast evaluation of protein energies directly from sequence. PLoS Comput Biol 2(6): e63.  ...  Second, the agreement between two full-atom methods that we tested and their CE sequence-based expressions is very high (root mean square deviation 1.1-4.7 kcal/mol, R 2 ¼ 0.7-1.0).  ...  is expressed as: f ðrÞ ¼ J 0 þ X i r i 6 ¼ 0 J i r i / r i ðr i Þ þ X i 6 ¼ j r i ; r j 6 ¼ 0 J ij r i r j / r i ðr i Þ/ r j ðr j Þ þ Á Á Á ¼ J 0 þ X i r i 6 ¼ 0 J i r i þ X i 6 ¼ j r i ; r j 6 ¼ 0 J  ... 
doi:10.1371/journal.pcbi.0020063.eor fatcat:shyxuf6ngbcxfluweotmjjx6la

Ultra-Fast Evaluation of Protein Energies Directly from Sequence

Gevorg Grigoryan, Fei Zhou, Steve R. Lustig, Gerbrand Ceder, Dane Morgan, Amy E. Keating
2006 PLoS Computational Biology  
Citation: Grigoryan G, Zhou F, Lustig SR, Ceder G, Morgan D, et al. (2006) Ultra-fast evaluation of protein energies directly from sequence. PLoS Comput Biol 2(6): e63.  ...  Second, the agreement between two full-atom methods that we tested and their CE sequence-based expressions is very high (root mean square deviation 1.1-4.7 kcal/mol, R 2 ¼ 0.7-1.0).  ...  is expressed as: f ðrÞ ¼ J 0 þ X i r i 6 ¼ 0 J i r i / r i ðr i Þ þ X i 6 ¼ j r i ; r j 6 ¼ 0 J ij r i r j / r i ðr i Þ/ r j ðr j Þ þ Á Á Á ¼ J 0 þ X i r i 6 ¼ 0 J i r i þ X i 6 ¼ j r i ; r j 6 ¼ 0 J  ... 
doi:10.1371/journal.pcbi.0020063 pmid:16789811 pmcid:PMC1479088 fatcat:k6qnybbkdfbpbc6422pxk7dnim

Coarse-Graining Protein Energetics in Sequence Variables

Fei Zhou, Gevorg Grigoryan, Steve R. Lustig, Amy E. Keating, Gerbrand Ceder, Dane Morgan
2005 Physical Review Letters  
We show that cluster expansions (CE), previously used to model solid-state materials with binary or ternary configurational disorder, can be extended to the protein design problem. We present a generalized CE framework, in which properties such as energy can be unambiguously expanded in the amino-acid sequence space. The CE coarse grains over nonsequence degrees of freedom (e.g., side-chain conformations) and thereby simplifies the problem of designing proteins, or predicting the compatibility
more » ... f a sequence with a given structure, by many orders of magnitude. The CE is physically transparent, and can be evaluated through linear regression on the energies of training sequences. We show, as example, that good prediction accuracy is obtained with up to pairwise interactions for a coiled-coil backbone, and that triplet interactions are important in the energetics of a more globular zinc-finger backbone.
doi:10.1103/physrevlett.95.148103 pmid:16241695 fatcat:7lqghxta5nfvzmeaa5jggl2r2u

Translating the Genomics Revolution: The Need for an International Gene Therapy Consortium for Monogenic Diseases

Jacques P Tremblay, Xiao Xiao, Annemieke Aartsma-Rus, Carlos Barbas, Helen M Blau, Adam J Bogdanove, Kym Boycott, Serge Braun, Xandra O Breakefield, Juan A Bueren, Michael Buschmann, Barry J Byrne (+39 others)
2013 Molecular Therapy  
doi:10.1038/mt.2013.4 pmid:23369965 pmcid:PMC3594019 fatcat:tw7iw4c4bvcsnjvnsshbviur7a

Page 235 of American Society of Civil Engineers. Collected Journals Vol. 9, Issue 4 [page]

1995 American Society of Civil Engineers. Collected Journals  
Army Corps of Engineers, for their support of this research project; Steve Stoner and Joe Pace, of the ARMS’s Technical Center of Expertise, for their advice and technical support; and to the programmers  ...  R: Base, user’s manual, Version 3.1, Redmond, Wash. Microsoft. (1991). Microsoft, C/C+ + user’s manual, Version 7.0, Red- mond, Wash. Reisbeck, S. (1989).  ... 

Page 2263 of Genetics Vol. 174, Issue 4 [page]

2006 Genetics  
Larsen, Pamela Larson, Greger Larson, Steve R. Larsson, Jan Lartillot, Nicolas Lascoux, Martin Lasko, Paul Laughon, Allen Lawrence, Jeffrey Lazzaro, Brian P.  ...  Lustig, Arthur Lydall, David Lyon, Elaine Lyttle, Terrence W. Ma, Hong Ma, Xue-Feng Macdonald, Stuart J. Machado, Carlos A. Mackem, Susan Macpherson, John M. Madura, Kiran  ... 

Page 35 of APCJ Faxnews Vol. 76, Issue 16 [page]

1991 APCJ Faxnews  
KOCH, ROBERT KOEHLER, STEVE KOSKI, CHRISTINE KOVAC, DANIEL KRINSKY, PETER KRUEGER, ROBERT A. KUMM, HERMAN KURFEES, DONALD B. KYTASAARI, LAWRENCE K. LAAKSO, THOMAS R. LAMB, JOHN LAMY, ALFRED LAM, S.  ...  BRENNAN, MICHAEL R. BRICKNELL, CAROLINE T. BRINCAT, LOUIS BROD, ROBERT A. BROLSMA, KEVIN BROWN, J.B. BRUDER JR., THOMAS A. BRUDER, JAMES J. BRUMMERHOP, JC. BRVENIK, JOHN R.  ... 

Page 35 of APCJ Faxnews Vol. 79, Issue 8 [page]

1994 APCJ Faxnews  
Williams, Robert A. and Mickey Williamson, Augustus Williamson, Richard and Elsie Wilson, John R. and Eva Winston, Steve Wint, Rufus F.  ...  Lum, Rolando Lurie, David Lustig, Stephen and Lee Lutz, George and Judy Lynam, Nicholas Maas, Joseph MacKinnon, Malcolm and Barbara Macway, Ken Maggio, Thomas E. and Beatrice Maio, Nick and Michelene Maisch  ... 

Page 32 of Detroit Institute of Arts. Bulletin of the Detroit Institute of Arts Vol. 31, Issue 2 [page]

1951 Detroit Institute of Arts. Bulletin of the Detroit Institute of Arts  
Adolph Cavallo, working with the Associated Cinematographers of Detroit, Adrian Lustig, Steve Bubel and W. C. Brame, wrote and directed a ten-minute color film, Venice in the 18th Century.  ...  Walter R. Agard, Dr. George Lechler, Dr. Karl Hersey, Adéle Coulin Weibel, Dr. Ernst Schever, and Francis W. Robinson.  ... 

Page 45 of Journal of Advertising Research Vol. 14, Issue 2 [page]

1974 Journal of Advertising Research  
Strickland, Ph.D., President Thomas R. Leggett, Executive Vice President Philip Lustig, Vice President research ¢ Full service organization You get both from mail surveys by Erdos and Morgan.  ...  Russell, President Clifford R. Knowles, Exec.  ... 

Page 11208 of Psychological Abstracts Vol. 91, Issue 4 [page]

2004 Psychological Abstracts  
., 9409 Lunt, Peter, 10070 Luo, Xingguang, 10798 Lupfer, Gwen, 9748 Lusher, Joanne, 10980 Lustig, Stuart L., 10830 Liithl, Andreas, 9746 Liitjohann, Dieter, 11308 Lutz, Piotr, 9992 Lux, Silke, 11649 Luzzatti  ...  E., 10133 McCoy, Shannon K., 10539 McCrea, Sean M.. 10529 McCreadie, R.  ... 

Page 4302 of Psychological Abstracts Vol. 91, Issue 11 [page]

2004 Psychological Abstracts  
D., 31385 McKeith, Ian G., 32555 McKenna, Steve, 33261 McKenzie, Craig R.  ...  Vande, 31219 Luo, Zupei, 31866 Lupart, Judy L., 33130 Lupfer, Michael B., 31463 Lush, Dora, 30552 Lustig, Deborah Freedman, 31232 Luszezynska, Aleksandra, 30413 Lutchmaya, S., 31114 Luterek, Jane A., 31593  ... 

Page 38 of APCJ Faxnews Vol. 78, Issue 17 [page]

1993 APCJ Faxnews  
Barbanel, Steve Barry, Ron and Ginger Beasley, Milam Beck, Peter B.  ...  Kallal, David Kane, Jack R. Karl, Erhard and Margi Kasprzak, Henry Keenan, James and Jo Ann Kehlhem, A.  ... 

Page 93 of American Chiropractic Association. The ACA Journal of Chiropractic Vol. 34, Issue 3 [page]

1997 American Chiropractic Association. The ACA Journal of Chiropractic  
Joseph, DC Santa Clara, California Steve N. Jukich, DC Spokane, Washington Brian D. Justice, DC Rochester, New York Michael T. Kambourelis, DC Palm Bay, Florida Keith R.  ...  Lustig, DC St Peters. Missouri Jeffrey R. Lyne, DC Sun Prairie, Wisconsin Paul F. Lyons, Jr, DC North Plainfield, New Jersey Gilbert A. Machacek, DC St Petersburg, Florida Jeffrey C.  ... 

Page 254 of Florida Bar Journal Vol. 73, Issue 8 [page]

1999 Florida Bar Journal  
Park NY 11729-2119 Fax: 516/667-0014 LUSTIG, Roy R . 305/442-1731 911 Dou^ Centre 26X S Douglas Rd Coral Gables 331346127 LUSTIG, Stephen Leslie ... 954/4691500 Lustg 6 Assocates 524 S Andrews Ave Ste  ...  MA 021165616 E-mail: clustig@fac.nesl.edu Fax: 617/422-7453 LUSTIG, Jordan R . 203/3691300 XI^Lala^e BNd Ste 509 Bridgeport CT 06604- LUSTIG, Leonard . 516/6676011 21X Dea Pak Ave 21X Deer Pak Ave Oeer  ... 
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