AlphaFold, artificial intelligence (AI), and allostery
R Nussinov, M Zhang, Y Liu, H Jang - The Journal of Physical …, 2022 - ACS Publications
AlphaFold has burst into our lives. A powerful algorithm that underscores the strength of
biological sequence data and artificial intelligence (AI). AlphaFold has appended projects …
biological sequence data and artificial intelligence (AI). AlphaFold has appended projects …
The impact of AlphaFold Protein Structure Database on the fields of life sciences
M Varadi, S Velankar - Proteomics, 2023 - Wiley Online Library
Arguably, 2020 was the year of high‐accuracy protein structure predictions, with AlphaFold
2.0 achieving previously unseen accuracy in the Critical Assessment of Protein Structure …
2.0 achieving previously unseen accuracy in the Critical Assessment of Protein Structure …
DALI shines a light on remote homologs: One hundred discoveries
Structural comparison reveals remote homology that often fails to be detected by sequence
comparison. The DALI web server (http://ekhidna2. biocenter. helsinki. fi/dali) is a platform …
comparison. The DALI web server (http://ekhidna2. biocenter. helsinki. fi/dali) is a platform …
Novel machine learning approaches revolutionize protein knowledge
Breakthrough methods in machine learning (ML), protein structure prediction, and novel
ultrafast structural aligners are revolutionizing structural biology. Obtaining accurate models …
ultrafast structural aligners are revolutionizing structural biology. Obtaining accurate models …
Tutorial: a guide for the selection of fast and accurate computational tools for the prediction of intrinsic disorder in proteins
Intrinsic disorder is instrumental for a wide range of protein functions, and its analysis, using
computational predictions from primary structures, complements secondary and tertiary …
computational predictions from primary structures, complements secondary and tertiary …
RCSB protein data bank: efficient searching and simultaneous access to one million computed structure models alongside the PDB structures enabled by architectural …
S Bittrich, C Bhikadiya, C Bi, H Chao, JM Duarte… - Journal of molecular …, 2023 - Elsevier
Abstract The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB
PDB) provides open access to experimentally-determined three-dimensional (3D) structures …
PDB) provides open access to experimentally-determined three-dimensional (3D) structures …
Csx28 is a membrane pore that enhances CRISPR-Cas13b–dependent antiphage defense
AR VanderWal, JU Park, B Polevoda, JK Nicosia… - Science, 2023 - science.org
Type VI CRISPR-Cas systems use RNA-guided ribonuclease (RNase) Cas13 to defend
bacteria against viruses, and some of these systems encode putative membrane proteins …
bacteria against viruses, and some of these systems encode putative membrane proteins …
TM-search: An efficient and effective tool for protein structure database search
The quickly increasing size of the Protein Data Bank is challenging biologists to develop a
more scalable protein structure alignment tool for fast structure database search. Although …
more scalable protein structure alignment tool for fast structure database search. Although …
[HTML][HTML] Beyond sequence: Structure-based machine learning
Recent breakthroughs in protein structure prediction demarcate the start of a new era in
structural bioinformatics. Combined with various advances in experimental structure …
structural bioinformatics. Combined with various advances in experimental structure …
[HTML][HTML] Assessing structure and disorder prediction tools for de novo emerged proteins in the age of machine learning
Background: De novo protein coding genes emerge from scratch in the non-coding regions
of the genome and have, per definition, no homology to other genes. Therefore, their …
of the genome and have, per definition, no homology to other genes. Therefore, their …