[HTML][HTML] Hybrid methods for combined experimental and computational determination of protein structure

JT Seffernick, S Lindert - The Journal of chemical physics, 2020 - pubs.aip.org
Knowledge of protein structure is paramount to the understanding of biological function,
developing new therapeutics, and making detailed mechanistic hypotheses. Therefore …

Protein crystallography for aspiring crystallographers or how to avoid pitfalls and traps in macromolecular structure determination

A Wlodawer, W Minor, Z Dauter… - The FEBS journal, 2013 - Wiley Online Library
The number of macromolecular structures deposited in the Protein Data Bank now
approaches 100 000, with the vast majority of them determined by crystallographic methods …

[PDF][PDF] Automated structure solution, density modification and model building

TC Terwilliger - Acta Crystallographica Section D: Biological …, 2002 - journals.iucr.org
The approaches that form the basis of automated structure solution in SOLVE and
RESOLVE are described. The use of a scoring scheme to convert decision making in …

The PDB format, mmCIF, and other data formats

JD Westbrook, PM Fitzgerald - Methods Biochem Anal, 2003 - Wiley Online Library
In this chapter, the data formats and protocols used to represent primary macromolecular
structure data are presented. The historical format used by the Protein Data Bank (PDB) is …

Optimization of crystallization conditions for biological macromolecules

A McPherson, B Cudney - Acta Crystallographica Section F …, 2014 - journals.iucr.org
For the successful X-ray structure determination of macromolecules, it is first necessary to
identify, usually by matrix screening, conditions that yield some sort of crystals. Initial crystals …

STAR/mmCIF: an ontology for macromolecular structure

JD Westbrook, PE Bourne - Bioinformatics, 2000 - academic.oup.com
Motivation: Crystallographers were motivated 10 years ago to develop a simple and
consistent data representation for the exchange and archiving of data associated with the …

Joint X-ray and neutron refinement with phenix. refine

PV Afonine, M Mustyakimov… - … Section D: Biological …, 2010 - journals.iucr.org
Approximately 85% of the structures deposited in the Protein Data Bank have been solved
using X-ray crystallography, making it the leading method for three-dimensional structure …

Integrating macromolecular X-ray diffraction data with the graphical user interface iMosflm

HR Powell, TGG Battye, L Kontogiannis, O Johnson… - Nature protocols, 2017 - nature.com
X-ray crystallography is the predominant source of structural information for biological
macromolecules, providing fundamental insights into biological function. The availability of …

xdlMAPMAN and xdlDATAMAN–programs for reformatting, analysis and manipulation of biomacromolecular electron-density maps and reflection data sets

GJ Kleywegt, TA Jones - Acta Crystallographica Section D: Biological …, 1996 - scripts.iucr.org
Two user-friendly computer programs are described for use in macromolecular X-ray
crystallography, xdlMAP-MAN provides an interface for electron-density map exchange …

Web-Ice: integrated data collection and analysis for macromolecular crystallography

A Gonzalez, P Moorhead, SE McPhillips… - Journal of Applied …, 2008 - journals.iucr.org
New software tools are introduced to facilitate diffraction experiments involving large
numbers of crystals. While existing programs have long provided a framework for lattice …