I-TASSER-MTD: a deep-learning-based platform for multi-domain protein structure and function prediction

X Zhou, W Zheng, Y Li, R Pearce, C Zhang, EW Bell… - Nature …, 2022 - nature.com
Most proteins in cells are composed of multiple folding units (or domains) to perform
complex functions in a cooperative manner. Relative to the rapid progress in single-domain …

Accurate prediction of protein structures and interactions using a three-track neural network

M Baek, F DiMaio, I Anishchenko, J Dauparas… - Science, 2021 - science.org
DeepMind presented notably accurate predictions at the recent 14th Critical Assessment of
Structure Prediction (CASP14) conference. We explored network architectures that …

Baculovirus molecular biology

GF Rohrmann - 2019 - ir.library.oregonstate.edu
This is the 4th edition of a book that was initiated with the annotation of the function of all the
genes in the most commonly studied baculovirus, AcMNPV. It has been almost six years …

Improved prediction of protein-protein interactions using AlphaFold2

P Bryant, G Pozzati, A Elofsson - Nature communications, 2022 - nature.com
Predicting the structure of interacting protein chains is a fundamental step towards
understanding protein function. Unfortunately, no computational method can produce …

Protein sequence analysis using the MPI bioinformatics toolkit

F Gabler, SZ Nam, S Till, M Mirdita… - Current Protocols in …, 2020 - Wiley Online Library
Abstract The MPI Bioinformatics Toolkit (https://toolkit. tuebingen. mpg. de) provides
interactive access to a wide range of the best‐performing bioinformatics tools and …

[HTML][HTML] An expanded arsenal of immune systems that protect bacteria from phages

A Millman, S Melamed, A Leavitt, S Doron… - Cell host & …, 2022 - cell.com
Bacterial anti-phage systems are frequently clustered in microbial genomes, forming
defense islands. This property enabled the recent discovery of multiple defense systems …

A functional selection reveals previously undetected anti-phage defence systems in the E. coli pangenome

CN Vassallo, CR Doering, ML Littlehale… - Nature …, 2022 - nature.com
The ancient, ongoing coevolutionary battle between bacteria and their viruses,
bacteriophages, has given rise to sophisticated immune systems including restriction …

The 2019‐new coronavirus epidemic: evidence for virus evolution

D Benvenuto, M Giovanetti, A Ciccozzi… - Journal of medical …, 2020 - Wiley Online Library
There is a worldwide concern about the new coronavirus 2019‐nCoV as a global public
health threat. In this article, we provide a preliminary evolutionary and molecular …

Mammalian retrovirus-like protein PEG10 packages its own mRNA and can be pseudotyped for mRNA delivery

M Segel, B Lash, J Song, A Ladha, CC Liu, X **… - Science, 2021 - science.org
Eukaryotic genomes contain domesticated genes from integrating viruses and mobile
genetic elements. Among these are homologs of the capsid protein (known as Gag) of long …

CheckV assesses the quality and completeness of metagenome-assembled viral genomes

S Nayfach, AP Camargo, F Schulz… - Nature …, 2021 - nature.com
Millions of new viral sequences have been identified from metagenomes, but the quality and
completeness of these sequences vary considerably. Here we present CheckV, an …