Nitrite oxidation in wastewater treatment: microbial adaptation and suppression challenges

Z Su, T Liu, J Guo, M Zheng - Environmental Science & …, 2023 - ACS Publications
Microbial nitrite oxidation is the primary pathway that generates nitrate in wastewater
treatment systems and can be performed by a variety of microbes: namely, nitrite-oxidizing …

Opportunities and challenges for machine learning-assisted enzyme engineering

J Yang, FZ Li, FH Arnold - ACS Central Science, 2024 - ACS Publications
Enzymes can be engineered at the level of their amino acid sequences to optimize key
properties such as expression, stability, substrate range, and catalytic efficiency─ or even to …

UCSF ChimeraX: Tools for structure building and analysis

EC Meng, TD Goddard, EF Pettersen… - Protein …, 2023 - Wiley Online Library
Advances in computational tools for atomic model building are leading to accurate models of
large molecular assemblies seen in electron microscopy, often at challenging resolutions of …

Mechanisms of antigen escape from BCMA-or GPRC5D-targeted immunotherapies in multiple myeloma

H Lee, S Ahn, R Maity, N Leblay, B Ziccheddu… - Nature medicine, 2023 - nature.com
B cell maturation antigen (BCMA) target loss is considered to be a rare event that mediates
multiple myeloma (MM) resistance to anti-BCMA chimeric antigen receptor T cell (CAR T) or …

Generalized biomolecular modeling and design with RoseTTAFold All-Atom

R Krishna, J Wang, W Ahern, P Sturmfels, P Venkatesh… - Science, 2024 - science.org
Deep-learning methods have revolutionized protein structure prediction and design but are
presently limited to protein-only systems. We describe RoseTTAFold All-Atom (RFAA), which …

TTD: Therapeutic Target Database describing target druggability information

Y Zhou, Y Zhang, D Zhao, X Yu, X Shen… - Nucleic acids …, 2024 - academic.oup.com
Target discovery is one of the essential steps in modern drug development, and the
identification of promising targets is fundamental for developing first-in-class drug. A variety …

AlphaFold Protein Structure Database in 2024: providing structure coverage for over 214 million protein sequences

M Varadi, D Bertoni, P Magana, U Paramval… - Nucleic acids …, 2024 - academic.oup.com
Abstract The AlphaFold Database Protein Structure Database (AlphaFold DB,
https://alphafold. ebi. ac. uk) has significantly impacted structural biology by amassing over …

Using evolutionary data to make sense of macromolecules with a “face‐lifted” ConSurf

B Yariv, E Yariv, A Kessel, G Masrati, AB Chorin… - Protein …, 2023 - Wiley Online Library
The ConSurf web‐sever for the analysis of proteins, RNA, and DNA provides a quick and
accurate estimate of the per‐site evolutionary rate among homologues. The analysis reveals …

The IUPHAR/BPS guide to PHARMACOLOGY in 2024

SD Harding, JF Armstrong, E Faccenda… - Nucleic acids …, 2024 - academic.oup.com
Abstract The IUPHAR/BPS Guide to PHARMACOLOGY (GtoPdb; https://www.
guidetopharmacology. org) is an open-access, expert-curated, online database that …

A method for multiple-sequence-alignment-free protein structure prediction using a protein language model

X Fang, F Wang, L Liu, J He, D Lin, Y Xiang… - Nature Machine …, 2023 - nature.com
Protein structure prediction pipelines based on artificial intelligence, such as AlphaFold2,
have achieved near-experimental accuracy. These advanced pipelines mainly rely on …