De novo protein design by deep network hallucination

I Anishchenko, SJ Pellock, TM Chidyausiku… - Nature, 2021 - nature.com
There has been considerable recent progress in protein structure prediction using deep
neural networks to predict inter-residue distances from amino acid sequences,–. Here we …

Anomalous diffraction in crystallographic phase evaluation

WA Hendrickson - Quarterly reviews of biophysics, 2014 - cambridge.org
X-ray diffraction patterns from crystals of biological macromolecules contain sufficient
information to define atomic structures, but atomic positions are inextricable without having …

Codon influence on protein expression in E. coli correlates with mRNA levels

G Boël, R Letso, H Neely, WN Price, KH Wong, M Su… - Nature, 2016 - nature.com
Degeneracy in the genetic code, which enables a single protein to be encoded by a
multitude of synonymous gene sequences, has an important role in regulating protein …

Exploring the relationships between protein sequence, structure and solubility

K Trainor, A Broom, EM Meiering - Current opinion in structural biology, 2017 - Elsevier
Aggregation can be thought of as a form of protein folding in which intermolecular
associations lead to the formation of large, insoluble assemblies. Various types of …

The Protein Model Portal—a comprehensive resource for protein structure and model information

J Haas, S Roth, K Arnold, F Kiefer, T Schmidt… - Database, 2013 - academic.oup.com
Abstract The Protein Model Portal (PMP) has been developed to foster effective use of 3D
molecular models in biomedical research by providing convenient and comprehensive …

Principles for designing proteins with cavities formed by curved β sheets

E Marcos, B Basanta, TM Chidyausiku, Y Tang… - Science, 2017 - science.org
Active sites and ligand-binding cavities in native proteins are often formed by curved β
sheets, and the ability to control β-sheet curvature would allow design of binding proteins …

Automated protein structure modeling with SWISS-MODEL Workspace and the Protein Model Portal

L Bordoli, T Schwede - Homology Modeling: Methods and Protocols, 2012 - Springer
Comparative protein structure modeling is a computational approach to build three-
dimensional structural models for proteins using experimental structures of related protein …

[HTML][HTML] A high through-put platform for recombinant antibodies to folded proteins

M Hornsby, M Paduch, S Miersch, A Sääf… - Molecular & Cellular …, 2015 - Elsevier
Antibodies are key reagents in biology and medicine, but commercial sources are rarely
recombinant and thus do not provide a permanent and renewable resource. Here, we …

Solubility-Weighted Index: fast and accurate prediction of protein solubility

BK Bhandari, PP Gardner, CS Lim - Bioinformatics, 2020 - academic.oup.com
Motivation Recombinant protein production is a widely used technique in the biotechnology
and biomedical industries, yet only a quarter of target proteins are soluble and can therefore …

Aspirin's active metabolite salicylic acid targets high mobility group box 1 to modulate inflammatory responses

HW Choi, M Tian, F Song, E Venereau, A Preti… - Molecular …, 2015 - Springer
Salicylic acid (SA) and its derivatives have been used for millennia to reduce pain, fever and
inflammation. In addition, prophylactic use of acetylsalicylic acid, commonly known as …