Daniel A Keedy
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Explore the profile of Daniel A Keedy including associated specialties, affiliations and a list of published articles.
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Recent Articles
21.
van Zundert G, Hudson B, P de Oliveira S, Keedy D, Fonseca R, Heliou A, et al.
J Med Chem
. 2018 Nov;
61(24):11183-11198.
PMID: 30457858
Proteins and ligands sample a conformational ensemble that governs molecular recognition, activity, and dissociation. In structure-based drug design, access to this conformational ensemble is critical to understand the balance between...
22.
Keedy D, Hill Z, Biel J, Kang E, Rettenmaier T, Brandao-Neto J, et al.
Elife
. 2018 Jun;
7.
PMID: 29877794
Allostery is an inherent feature of proteins, but it remains challenging to reveal the mechanisms by which allosteric signals propagate. A clearer understanding of this intrinsic circuitry would afford new...
23.
Williams C, Headd J, Moriarty N, Prisant M, Videau L, Deis L, et al.
Protein Sci
. 2017 Oct;
27(1):293-315.
PMID: 29067766
This paper describes the current update on macromolecular model validation services that are provided at the MolProbity website, emphasizing changes and additions since the previous review in 2010. There have...
24.
Russi S, Gonzalez A, Kenner L, Keedy D, Fraser J, van den Bedem H
J Synchrotron Radiat
. 2016 Dec;
24(Pt 1):73-82.
PMID: 28009548
Protein crystallography data collection at synchrotrons is routinely carried out at cryogenic temperatures to mitigate radiation damage. Although damage still takes place at 100 K and below, the immobilization of...
25.
Cimermancic P, Weinkam P, Rettenmaier T, Bichmann L, Keedy D, Woldeyes R, et al.
J Mol Biol
. 2016 Feb;
428(4):709-719.
PMID: 26854760
Many proteins have small-molecule binding pockets that are not easily detectable in the ligand-free structures. These cryptic sites require a conformational change to become apparent; a cryptic site can therefore...
26.
Keedy D, Fraser J, van den Bedem H
PLoS Comput Biol
. 2015 Oct;
11(10):e1004507.
PMID: 26506617
Proteins must move between different conformations of their native ensemble to perform their functions. Crystal structures obtained from high-resolution X-ray diffraction data reflect this heterogeneity as a spatial and temporal...
27.
Keedy D, Kenner L, Warkentin M, Woldeyes R, Hopkins J, Thompson M, et al.
Elife
. 2015 Oct;
4.
PMID: 26422513
Determining the interconverting conformations of dynamic proteins in atomic detail is a major challenge for structural biology. Conformational heterogeneity in the active site of the dynamic enzyme cyclophilin A (CypA)...
28.
Keedy D
Proteins
. 2015 Jan;
83(5):797-8.
PMID: 25619796
Protein structures are often thought of as static objects, and indeed, the bulk of a protein's sequence forms α-helices, β-sheets, and other generally well-ordered substructures. These portions of the molecule...
29.
Keedy D, van den Bedem H, Sivak D, Petsko G, Ringe D, Wilson M, et al.
Structure
. 2014 Jun;
22(6):899-910.
PMID: 24882744
Most macromolecular X-ray structures are determined from cryocooled crystals, but it is unclear whether cryocooling distorts functionally relevant flexibility. Here we compare independently acquired pairs of high-resolution data sets of...
30.
Gainza P, Roberts K, Georgiev I, Lilien R, Keedy D, Chen C, et al.
Methods Enzymol
. 2013 Feb;
523:87-107.
PMID: 23422427
Unlabelled: We have developed a suite of protein redesign algorithms that improves realistic in silico modeling of proteins. These algorithms are based on three characteristics that make them unique: (1)...