Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently

A Currin, N Swainston, PJ Day, DB Kell - Chemical Society Reviews, 2015 - pubs.rsc.org
The amino acid sequence of a protein affects both its structure and its function. Thus, the
ability to modify the sequence, and hence the structure and activity, of individual proteins in …

Renal function in newly diagnosed multiple myeloma—a demographic study of 1353 patients

LM Knudsen, E Hippe, M Hjorth… - European journal of …, 1994 - Wiley Online Library
This study describes the occurrence of renal failure among 1353 newly diagnosed cases of
multiple myeloma. Renal function was evaluated by serum creatinine concentration in 1353 …

How significant is a protein structure similarity with TM-score= 0.5?

J Xu, Y Zhang - Bioinformatics, 2010 - academic.oup.com
Motivation: Protein structure similarity is often measured by root mean squared deviation,
global distance test score and template modeling score (TM-score). However, the scores …

Advances and pitfalls of protein structural alignment

H Hasegawa, L Holm - Current opinion in structural biology, 2009 - Elsevier
Structure comparison opens a window into the distant past of protein evolution, which has
been unreachable by sequence comparison alone. With 55000 entries in the Protein Data …

Low‐density lipoprotein receptor gene familial hypercholesterolemia variant database: update and pathological assessment

E Usifo, SEA Leigh, RA Whittall, N Lench… - Annals of human …, 2012 - Wiley Online Library
Familial hypercholesterolemia (FH) is caused predominately by variants in the low‐density
lipoprotein receptor gene (LDLR). We report here an update of the UCL LDLR variant …

Druggable pockets and binding site centric chemical space: a paradigm shift in drug discovery

S Pérot, O Sperandio, MA Miteva, AC Camproux… - Drug discovery today, 2010 - Elsevier
Detection, comparison and analyses of binding pockets are pivotal to structure-based drug
design endeavors, from hit identification, screening of exosites and de-orphanization of …

Exploring structural diversity across the protein universe with The Encyclopedia of Domains

AM Lau, N Bordin, SM Kandathil, I Sillitoe, VP Waman… - Science, 2024 - science.org
The AlphaFold Protein Structure Database (AFDB) contains more than 214 million predicted
protein structures composed of domains, which are independently folding units found in …

The Protein Data Bank archive as an open data resource

HM Berman, GJ Kleywegt, H Nakamura… - Journal of computer …, 2014 - Springer
Abstract The Protein Data Bank archive was established in 1971, and recently celebrated its
40th anniversary (Berman et al. in Structure 20: 391, 2012). An analysis of interrelationships …

ASD: a comprehensive database of allosteric proteins and modulators

Z Huang, L Zhu, Y Cao, G Wu, X Liu… - Nucleic acids …, 2011 - academic.oup.com
Allostery is the most direct, rapid and efficient way of regulating protein function, ranging
from the control of metabolic mechanisms to signal-transduction pathways. However, an …

Heme proteins—diversity in structural characteristics, function, and folding

LJ Smith, A Kahraman… - … : structure, function, and …, 2010 - Wiley Online Library
The characteristics of heme prosthetic groups and their binding sites have been analyzed in
detail in a data set of nonhomologous heme proteins. Variations in the shape, volume, and …