Andrew Leaver-Fay
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Explore the profile of Andrew Leaver-Fay including associated specialties, affiliations and a list of published articles.
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29
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6045
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Recent Articles
11.
Leaver-Fay A, Froning K, Atwell S, Aldaz H, Pustilnik A, Lu F, et al.
Structure
. 2016 Mar;
24(4):641-651.
PMID: 26996964
A challenge in the structure-based design of specificity is modeling the negative states, i.e., the complexes that you do not want to form. This is a difficult problem because mutations...
12.
Combined covalent-electrostatic model of hydrogen bonding improves structure prediction with Rosetta
OMeara M, Leaver-Fay A, Tyka M, Stein A, Houlihan K, DiMaio F, et al.
J Chem Theory Comput
. 2015 Apr;
11(2):609-22.
PMID: 25866491
Interactions between polar atoms are challenging to model because at very short ranges they form hydrogen bonds (H-bonds) that are partially covalent in character and exhibit strong orientation preferences; at...
13.
Jacobs T, Yumerefendi H, Kuhlman B, Leaver-Fay A
Nucleic Acids Res
. 2014 Dec;
43(5):e34.
PMID: 25539925
Degenerate codon (DC) libraries efficiently address the experimental library-size limitations of directed evolution by focusing diversity toward the positions and toward the amino acids (AAs) that are most likely to...
14.
Lewis S, Wu X, Pustilnik A, Sereno A, Huang F, Rick H, et al.
Nat Biotechnol
. 2014 Jan;
32(2):191-8.
PMID: 24463572
Robust generation of IgG bispecific antibodies has been a long-standing challenge. Existing methods require extensive engineering of each individual antibody, discovery of common light chains, or complex and laborious biochemical...
15.
Drew K, Renfrew P, Craven T, Butterfoss G, Chou F, Lyskov S, et al.
PLoS One
. 2013 Jul;
8(7):e67051.
PMID: 23869206
Peptidomimetics are classes of molecules that mimic structural and functional attributes of polypeptides. Peptidomimetic oligomers can frequently be synthesized using efficient solid phase synthesis procedures similar to peptide synthesis. Conformationally...
16.
Leaver-Fay A, OMeara M, Tyka M, Jacak R, Song Y, Kellogg E, et al.
Methods Enzymol
. 2013 Feb;
523:109-43.
PMID: 23422428
Accurate energy functions are critical to macromolecular modeling and design. We describe new tools for identifying inaccuracies in energy functions and guiding their improvement, and illustrate the application of these...
17.
Jacak R, Leaver-Fay A, Kuhlman B
Proteins
. 2012 Jan;
80(3):825-38.
PMID: 22223219
De novo protein design requires the identification of amino-acid sequences that favor the target-folded conformation and are soluble in water. One strategy for promoting solubility is to disallow hydrophobic residues...
18.
Leaver-Fay A, Jacak R, Stranges P, Kuhlman B
PLoS One
. 2011 Jul;
6(7):e20937.
PMID: 21754981
Some protein design tasks cannot be modeled by the traditional single state design strategy of finding a sequence that is optimal for a single fixed backbone. Such cases require multistate...
19.
DiMaio F, Leaver-Fay A, Bradley P, Baker D, Andre I
PLoS One
. 2011 Jul;
6(6):e20450.
PMID: 21731614
Symmetric protein assemblies play important roles in many biochemical processes. However, the large size of such systems is challenging for traditional structure modeling methods. This paper describes the implementation of...
20.
Fleishman S, Leaver-Fay A, Corn J, Strauch E, Khare S, Koga N, et al.
PLoS One
. 2011 Jul;
6(6):e20161.
PMID: 21731610
Macromolecular modeling and design are increasingly useful in basic research, biotechnology, and teaching. However, the absence of a user-friendly modeling framework that provides access to a wide range of modeling...