David C. Richardson

Journal article Proc Natl Acad Sci U S A · March 5, 2002 Featured Publication The fact that natural beta-sheet proteins are usually soluble but that fragments or designs of beta structure usually aggregate suggests that natural beta proteins must somehow be designed to avoid this problem. Regular beta-sheet edges are dangerous, beca ... Full text Link to item Cite

Exploring steric constraints on protein mutations using MAGE/PROBE.

Journal article Protein Sci · November 2000 Featured Publication When planning a mutation to test some hypothesis, one crucial question is whether the new side chain is compatible with the existing structure; only if it is compatible can the interpretation of mutational results be straightforward. This paper presents a ... Full text Link to item Cite

The penultimate rotamer library.

Journal article Proteins · August 15, 2000 Featured Publication All published rotamer libraries contain some rotamers that exhibit impossible internal atomic overlaps if built in ideal geometry with all hydrogen atoms. Removal of uncertain residues (mainly those with B-factors >/=40 or van der Waals overlaps >/=0.4 A) ... Link to item Cite

SymROP: ROP protein with identical helices redesigned by all-atom contact analysis and molecular dynamics.

Journal article J Mol Graph Model · June 2000 Featured Publication Experience has shown that protein redesigns (using the backbone from a known protein structure) are far more likely to produce well-ordered, native-like structures than are true de novo designs. Therefore, to design a four-helix bundle made of identical sh ... Full text Link to item Cite

Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms.

Journal article J Mol Biol · January 29, 1999 Featured Publication The technique of small-probe contact dot surfaces is described as a method for calculating and displaying the detailed atomic contacts inside or between molecules. It allows one both to measure and to visualize directly the goodness-of-fit of packing inter ... Full text Link to item Cite

Asparagine and glutamine rotamers: B-factor cutoff and correction of amide flips yield distinct clustering.

Journal article Proc Natl Acad Sci U S A · January 19, 1999 Featured Publication Previous rotamer libraries showed little significant clustering for asparagine chi2 or glutamine chi3 values, but none of those studies corrected amide orientations or omitted disordered side chains. The current survey used 240 proteins at Full text Link to item Cite

The Alacoil: a very tight, antiparallel coiled-coil of helices.

Journal article Protein Sci · November 1995 Featured Publication The Alacoil is an antiparallel (rather than the usual parallel) coiled-coil of alpha-helices with Ala or another small residue in every seventh position, allowing a very close spacing of the helices (7.5-8.5 A between local helix axes), often over four or ... Full text Link to item Cite

Sculpting proteins interactively: continual energy minimization embedded in a graphical modeling system.

Journal article Protein Sci · February 1994 Featured Publication We describe a new paradigm for modeling proteins in interactive computer graphics systems--continual maintenance of a physically valid representation, combined with direct user control and visualization. This is achieved by a fast algorithm for energy mini ... Full text Link to item Cite

The kinemage: a tool for scientific communication.

Journal article Protein Sci · January 1992 Featured Publication A "kinemage" (kinetic image) is a scientific illustration presented as an interactive computer display. Operations on the displayed kinemage respond within a fraction of a second: the entire image can be rotated in real time, parts of the display can be tu ... Full text Link to item Cite

De novo design, expression, and characterization of Felix: a four-helix bundle protein of native-like sequence.

Journal article Science · August 24, 1990 Featured Publication The protein Felix was designed de novo to fold into an antiparallel four-helix bundle of specific topology. Its sequence of 79 amino acid residues is not homologous to any known protein sequence, but is "native-like" in that it is nonrepetitive and contain ... Full text Link to item Cite

Amino acid preferences for specific locations at the ends of alpha helices.

Journal article Science · June 17, 1988 Featured Publication A definition based on alpha-carbon positions and a sample of 215 alpha helices from 45 different globular protein structures were used to tabulate amino acid preferences for 16 individual positions relative to the helix ends. The interface residue, which i ... Full text Link to item Cite

The heme and Fe4S4 cluster in the crystallographic structure of Escherichia coli sulfite reductase.

Journal article J Biol Chem · August 5, 1986 Featured Publication Isolated hemoprotein subunits of Escherichia coli NADPH:sulfite reductase catalyze the 6-electron reduction of SO2-3 to S2-. The prosthetic groups of the hemoprotein, a siroheme and a Fe4S4 cluster, have been shown by spectroscopy to be tightly coupled. We ... Link to item Cite

Determination and analysis of the 2 A-structure of copper, zinc superoxide dismutase.

Journal article J Mol Biol · September 15, 1982 Featured Publication Full text Link to item Cite

A high resolution structure of an inhibitor complex of the extracellular nuclease of Staphylococcus aureus. I. Experimental procedures and chain tracing.

Journal article J Biol Chem · April 10, 1971 Featured Publication Link to item Cite