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Primary Publication
This publication represents a primary interest of the Baker lab
Efficient sampling of protein conformational space using fast loop building and batch minimization on highly parallel computers.
Tyka, M. D.
,
Jung K.
, &
Baker D.
(2012).
Efficient sampling of protein conformational space using fast loop building and batch minimization on highly parallel computers.
.
Journal of computational chemistry. 33
(31), 2483-91.
Primary Publication
PubMed
Computational design of catalytic dyads and oxyanion holes for ester hydrolysis.
Richter, F.
,
Blomberg R.
,
Khare S. D.
,
Kiss G.
,
Kuzin A. P.
,
Smith A. J. T.
, et al.
(2012).
Computational design of catalytic dyads and oxyanion holes for ester hydrolysis.
.
Journal of the American Chemical Society. 134
(39), 16197-206.
Primary Publication
PubMed
Evaluation and optimization of discrete state models of protein folding.
Kellogg, E. H.
,
Lange O. F.
, &
Baker D.
(2012).
Evaluation and optimization of discrete state models of protein folding.
.
The journal of physical chemistry. B. 116
(37), 11405-13.
Primary Publication
PubMed
Computational design of self-assembling protein nanomaterials with atomic level accuracy
King, N. P.
,
Sheffler W.
,
Sawaya M. R.
,
Vollmar B. S.
,
Sumida J. P.
,
André I.
, et al.
(2012).
Computational design of self-assembling protein nanomaterials with atomic level accuracy
.
Science.
Primary Publication
1 attachment
Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing
Whitehead, T. A.
,
Chevalier A.
,
Song Y.
,
Dreyfus C.
,
Fleishman S. J.
,
De Mattos C.
, et al.
(2012).
Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing
.
Nature biotechnology.
Primary Publication
1 attachment
PubMed
Mining endonuclease cleavage determinants in genomic sequence data.
Szeto, M. D.
,
Boissel S. J. S.
,
Baker D.
, &
Thyme S. B.
(2011).
Mining endonuclease cleavage determinants in genomic sequence data.
.
The Journal of biological chemistry. 286
(37), 32617-27.
Primary Publication
PubMed
Crystal structure of a monomeric retroviral protease solved by protein folding game players
Khatib, F.
,
DiMaio F.
,
Cooper S.
,
Kazmierczyk M.
,
Gilski M.
,
Krzywda S.
, et al.
(2011).
Crystal structure of a monomeric retroviral protease solved by protein folding game players
.
Nature structural & molecular biology. 18
(10), 1175-7.
Primary Publication
1 attachment
PubMed
Increased Diels-Alderase activity through backbone remodeling guided by Foldit players
Eiben, C. B.
,
Siegel J. B.
,
Bale J. B.
,
Cooper S.
,
Khatib F.
,
Shen B. W.
, et al.
(2012).
Increased Diels-Alderase activity through backbone remodeling guided by Foldit players
.
Nature biotechnology. 30
(2), 190-2.
Primary Publication
1 attachment
PubMed
Structural analyses of covalent enzyme-substrate analog complexes reveal strengths and limitations of de novo enzyme design
Wang, L.
,
Althoff E. A.
,
Bolduc J.
,
Jiang L.
,
Moody J.
,
Lassila J. K.
, et al.
(2012).
Structural analyses of covalent enzyme-substrate analog complexes reveal strengths and limitations of de novo enzyme design
.
Journal of molecular biology. 415
(3), 615-25.
Primary Publication
1 attachment
PubMed
Computational redesign of a mononuclear zinc metalloenzyme for organophosphate hydrolysis
Khare, S. D.
,
Kipnis Y.
,
Greisen P. J.
,
Takeuchi R.
,
Ashani Y.
,
Goldsmith M.
, et al.
(2012).
Computational redesign of a mononuclear zinc metalloenzyme for organophosphate hydrolysis
.
Nature chemical biology.
Primary Publication
1 attachment
PubMed
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