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 …

Protein conformational ensembles in function: roles and mechanisms

R Nussinov, Y Liu, W Zhang, H Jang - RSC chemical biology, 2023 - pubs.rsc.org
The sequence-structure-function paradigm has dominated twentieth century molecular
biology. The paradigm tacitly stipulated that for each sequence there exists a single, well …

Bioinspired catalyst design principles: progress in emulating properties of enzymes in synthetic catalysts

B Ginovska, OY Gutiérrez, A Karkamkar, MS Lee… - ACS …, 2023 - ACS Publications
Catalysis enables many aspects of modern life, including fuels, products, plastics, and
medicines. Recent advances in catalysis have enabled us to realize higher efficiencies and …

Computing allostery: from the understanding of biomolecular regulation and the discovery of cryptic sites to molecular design

G Colombo - Current Opinion in Structural Biology, 2023 - Elsevier
The concept of allostery has become a central tenet in the study of biological systems. In
parallel, the discovery of allosteric drugs is generating new opportunities to selectively …

CDK2 and CDK4: Cell cycle functions evolve distinct, catalysis-competent conformations, offering drug targets

W Zhang, Y Liu, H Jang, R Nussinov - JACS Au, 2024 - ACS Publications
Cyclin-dependent kinases (CDKs), particularly CDK4 and CDK2, are crucial for cell cycle
progression from the Gap 1 (G1) to the Synthesis (S) phase by phosphorylating targets such …

Allosteric drugs: New principles and design approaches

WV Tee, IN Berezovsky - Current Opinion in Structural Biology, 2024 - Elsevier
Focusing on an important biomedical implication of allostery–design of allosteric drugs, we
describe characteristics of allosteric sites, effectors, and their modes of actions …

Molecular glues and induced proximity: An evolution of tools and discovery

SA Robinson, SM Banik - Cell Chemical Biology, 2024 - cell.com
Small molecule molecular glues can nucleate protein complexes and rewire interactomes.
Molecular glues are widely used as probes for understanding functional proximity at a …

Designing drugs and chemical probes with the dualsteric approach

J Zha, J He, C Wu, M Zhang, X Liu… - Chemical Society Reviews, 2023 - pubs.rsc.org
Traditionally, drugs are monovalent, targeting only one site on the protein surface. This
includes orthosteric and allosteric drugs, which bind the protein at orthosteric and allosteric …

DeepAlloDriver: a deep learning-based strategy to predict cancer driver mutations

Q Song, M Li, Q Li, X Lu, K Song, Z Zhang… - Nucleic acids …, 2023 - academic.oup.com
Driver mutations can contribute to the initial processes of cancer, and their identification is
crucial for understanding tumorigenesis as well as for molecular drug discovery and …

[HTML][HTML] Allostery frustrates the experimentalist

S Gianni, P Jemth - Journal of Molecular Biology, 2023 - Elsevier
Proteins interact with other proteins, with nucleic acids, lipids, carbohydrates and various
small molecules in the living cell. These interactions have been quantified and structurally …