Pathogenic or not? And if so, then how? Studying the effects of missense mutations using bioinformatics methods

J Thusberg, M Vihinen - Human mutation, 2009 - Wiley Online Library
Many gene defects are relatively easy to identify experimentally, but obtaining information
about the effects of sequence variations and elucidation of the detailed molecular …

Principles for designing ideal protein structures

N Koga, R Tatsumi-Koga, G Liu, R Xiao, TB Acton… - Nature, 2012 - nature.com
Unlike random heteropolymers, natural proteins fold into unique ordered structures.
Understanding how these are encoded in amino-acid sequences is complicated by …

Structure validation by Cα geometry: ϕ, ψ and Cβ deviation

SC Lovell, IW Davis, WB Arendall III… - Proteins: Structure …, 2003 - Wiley Online Library
Geometrical validation around the C is described, with a new C measure and updated
Ramachandran plot. Deviation of the observed C atom from ideal position provides a single …

Evaluating protein structures determined by structural genomics consortia

A Bhattacharya, R Tejero… - … : Structure, Function, and …, 2007 - Wiley Online Library
Structural genomics projects are providing large quantities of new 3D structural data for
proteins. To monitor the quality of these data, we have developed the protein structure …

Consistent blind protein structure generation from NMR chemical shift data

Y Shen, O Lange, F Delaglio, P Rossi… - Proceedings of the …, 2008 - National Acad Sciences
Protein NMR chemical shifts are highly sensitive to local structure. A robust protocol is
described that exploits this relation for de novo protein structure generation, using as input …

Natural β-sheet proteins use negative design to avoid edge-to-edge aggregation

JS Richardson, DC Richardson - Proceedings of the …, 2002 - National Acad Sciences
The fact that natural β-sheet proteins are usually soluble but that fragments or designs of β
structure usually aggregate suggests that natural β proteins must somehow be designed to …

De novo protein design by citizen scientists

B Koepnick, J Flatten, T Husain, A Ford, DA Silva… - Nature, 2019 - nature.com
Online citizen science projects such as GalaxyZoo, Eyewire and Phylo have proven very
successful for data collection, annotation and processing, but for the most part have …

[PDF][PDF] Use of knowledge-based restraints in phenix. refine to improve macromolecular refinement at low resolution

JJ Headd, N Echols, PV Afonine… - … Section D: Biological …, 2012 - journals.iucr.org
Traditional methods for macromolecular refinement often have limited success at low
resolution (3.0–3.5 Å or worse), producing models that score poorly on crystallographic and …

Automated analysis of protein NMR assignments and structures

MC Baran, YJ Huang, HNB Moseley… - Chemical …, 2004 - ACS Publications
A powerful feature of macromolecular structure analysis by NMR spectroscopy is its potential
for automation. 1, 2 It has been recognized for some time that many of the interactive tasks …

The backrub motion: how protein backbone shrugs when a sidechain dances

IW Davis, WB Arendall, DC Richardson, JS Richardson - Structure, 2006 - cell.com
Surprisingly, the frozen structures from ultra-high-resolution protein crystallography reveal a
prevalent, but subtle, mode of local backbone motion coupled to much larger, two-state …