Protein data bank: a comprehensive review of 3D structure holdings and worldwide utilization by researchers, educators, and students

SK Burley, HM Berman, JM Duarte, Z Feng, JW Flatt… - Biomolecules, 2022 - mdpi.com
The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB),
funded by the United States National Science Foundation, National Institutes of Health, and …

Modelling three-dimensional protein structures for applications in drug design

T Schmidt, A Bergner, T Schwede - Drug discovery today, 2014 - Elsevier
Highlights•The majority of proteins encoded in a genome are accessible by structure
modelling.•Modelling can provide accurate target predictions for structure-based drug …

QMEANDisCo—distance constraints applied on model quality estimation

G Studer, C Rempfer, AM Waterhouse… - …, 2020 - academic.oup.com
Motivation Methods that estimate the quality of a 3D protein structure model in absence of an
experimental reference structure are crucial to determine a model's utility and potential …

SWISS-MODEL: homology modelling of protein structures and complexes

A Waterhouse, M Bertoni, S Bienert… - Nucleic acids …, 2018 - academic.oup.com
Homology modelling has matured into an important technique in structural biology,
significantly contributing to narrowing the gap between known protein sequences and …

ProMod3—A versatile homology modelling toolbox

G Studer, G Tauriello, S Bienert, M Biasini… - PLoS computational …, 2021 - journals.plos.org
Computational methods for protein structure modelling are routinely used to complement
experimental structure determination, thus they help to address a broad spectrum of …

Modeling protein quaternary structure of homo-and hetero-oligomers beyond binary interactions by homology

M Bertoni, F Kiefer, M Biasini, L Bordoli, T Schwede - Scientific reports, 2017 - nature.com
Cellular processes often depend on interactions between proteins and the formation of
macromolecular complexes. The impairment of such interactions can lead to deregulation of …

The SWISS-MODEL Repository—new features and functionality

S Bienert, A Waterhouse, TAP De Beer… - Nucleic acids …, 2017 - academic.oup.com
Abstract SWISS-MODEL Repository (SMR) is a database of annotated 3D protein structure
models generated by the automated SWISS-MODEL homology modeling pipeline. It …

SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information

M Biasini, S Bienert, A Waterhouse… - Nucleic acids …, 2014 - academic.oup.com
Protein structure homology modelling has become a routine technique to generate 3D
models for proteins when experimental structures are not available. Fully automated servers …

Prediction of protein structures, functions and interactions using the IntFOLD7, MultiFOLD and ModFOLDdock servers

LJ McGuffin, NS Edmunds, AG Genc… - Nucleic acids …, 2023 - academic.oup.com
The IntFOLD server based at the University of Reading has been a leading method over the
past decade in providing free access to accurate prediction of protein structures and …

Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database

A Bissett, A Fitzgerald, T Meintjes, PM Mele, F Reith… - GigaScience, 2016 - Springer
Background Microbial inhabitants of soils are important to ecosystem and planetary
functions, yet there are large gaps in our knowledge of their diversity and ecology. The …