Remarks about protein structure precision

DWJ Cruickshank - Acta Crystallographica Section D: Biological …, 1999 - journals.iucr.org
Full-matrix least squares is taken as the basis for an examination of protein structure
precision. A two-atom protein model is used to compare the precisions of unrestrained and …

Application and limitations of X‐ray crystallographic data in structure‐based ligand and drug design

AM Davis, SJ Teague… - Angewandte Chemie …, 2003 - Wiley Online Library
Abstract Structure‐based design usually focuses upon the optimization of ligand affinity.
However, successful drug design also requires the optimization of many other properties …

Water molecules at protein–drug interfaces: computational prediction and analysis methods

ML Samways, RD Taylor, HEB Macdonald… - Chemical Society …, 2021 - pubs.rsc.org
The fundamental importance of water molecules at drug–protein interfaces is now widely
recognised and a significant feature in structure-based drug design. Experimental methods …

Experimentally observed conformation‐dependent geometry and hidden strain in proteins

PA Karplus - Protein Science, 1996 - Wiley Online Library
A database has been compiled documenting the peptide conformations and geometries
from 70 diverse proteins refined at 1.75 Å or better. Analysis of the well‐ordered residues …

Structures of the high-valent metal-ion haem–oxygen intermediates in peroxidases, oxygenases and catalases

HP Hersleth, U Ryde, P Rydberg, CH Görbitz… - Journal of inorganic …, 2006 - Elsevier
Peroxidases, oxygenases and catalases have similar high-valent metal-ion intermediates in
their respective reaction cycles. In this review, haem-based examples will be discussed. The …

Enhancing sampling of water rehydration on ligand binding: a comparison of techniques

Y Ge, DC Wych, ML Samways, ME Wall… - Journal of chemical …, 2022 - ACS Publications
Water often plays a key role in protein structure, molecular recognition, and mediating
protein–ligand interactions. Thus, free energy calculations must adequately sample water …

Reversible lattice repacking illustrates the temperature dependence of macromolecular interactions

DH Juers, BW Matthews - Journal of molecular biology, 2001 - Elsevier
Flash-freezing, which has become routine in macromolecular X-ray crystallography, causes
the crystal to contract substantially. In the case of Escherichia coli β-galactosidase the …

Quantum chemistry can locally improve protein crystal structures

U Ryde, K Nilsson - Journal of the American Chemical Society, 2003 - ACS Publications
We have re-refined the X-ray structure of the heme site in cytochrome c 553, supplementing
the crystallographic data with quantum chemical geometry optimizations, instead of the …

Large-scale networks of hydration water molecules around bovine β-trypsin revealed by cryogenic X-ray crystal structure analysis

M Nakasako - Journal of molecular biology, 1999 - Elsevier
The hydration structure of bovine β-trypsin was investigated in cryogenic X-ray diffraction
experiments. Three crystal forms of the enzyme inhibited by benzamidine with different …

The Protein Data Bank (PDB), its related services and software tools as key components for in silico guided drug discovery

J Kirchmair, P Markt, S Distinto… - Journal of medicinal …, 2008 - ACS Publications
In 1970, at a time when structural information of one atom was stored on a single punched
card, the crystallographers Helen M. Berman, Edgar Meyer, and Gerson Cohen began …