Along the allostery stream: Recent advances in computational methods for allosteric drug discovery

D Ni, Z Chai, Y Wang, M Li, Z Yu, Y Liu… - Wiley …, 2022 - Wiley Online Library
Allostery is a universal, biological phenomenon in which orthosteric sites are fine‐tuned by
topologically distal allosteric sites triggered by perturbations, such as ligand binding, residue …

Precision medicine and driver mutations: computational methods, functional assays and conformational principles for interpreting cancer drivers

R Nussinov, H Jang, CJ Tsai… - PLoS computational …, 2019 - journals.plos.org
At the root of the so-called precision medicine or precision oncology, which is our focus
here, is the hypothesis that cancer treatment would be considerably better if therapies were …

Mapping allosteric communications within individual proteins

J Wang, A Jain, LR McDonald, C Gambogi… - Nature …, 2020 - nature.com
Allostery in proteins influences various biological processes such as regulation of gene
transcription and activities of enzymes and cell signaling. Computational approaches for …

Structural basis of response regulator function

R Gao, S Bouillet, AM Stock - Annual review of microbiology, 2019 - annualreviews.org
Response regulators function as the output components of two-component systems, which
couple the sensing of environmental stimuli to adaptive responses. Response regulators …

[HTML][HTML] Intrinsic dynamics is evolutionarily optimized to enable allosteric behavior

Y Zhang, P Doruker, B Kaynak, S Zhang… - Current opinion in …, 2020 - Elsevier
Highlights•The intrinsic dynamics, encoded in proteins' sequences and structures, are
utilized by stimuli to trigger allosteric and functional actions.•The modes of allosteric actions …

Rational design of allosteric modulators: Challenges and successes

A Chatzigoulas, Z Cournia - Wiley Interdisciplinary Reviews …, 2021 - Wiley Online Library
Recent advances in structural biology and computational techniques have revealed
allosteric mechanisms for an abundance of targets leading to the establishment of rational …

Allosteric drugs and mutations: chances, challenges, and necessity

E Guarnera, IN Berezovsky - Current opinion in structural biology, 2020 - Elsevier
Highlights•Allosteric drugs have become an indispensable tool in precision medicine.•Major
targets for allosteric drugs: diversity structures and functions.•Allosteric effects of mutations …

Architecture and coevolution of allosteric materials

L Yan, R Ravasio, C Brito… - Proceedings of the …, 2017 - National Acad Sciences
We introduce a numerical scheme to evolve functional elastic materials that can accomplish
a specified mechanical task. In this scheme, the number of solutions, their spatial …

PASSer: Prediction of allosteric sites server

H Tian, X Jiang, P Tao - Machine learning: science and …, 2021 - iopscience.iop.org
Allostery is considered important in regulating protein's activity. Drug development depends
on the understanding of allosteric mechanisms, especially the identification of allosteric …

Applying structure-based drug design approaches to allosteric modulators of GPCRs

M Congreve, C Oswald, FH Marshall - Trends in pharmacological sciences, 2017 - cell.com
Structural insights have been revealed from X-ray co-complexes of a range of G protein-
coupled receptors (GPCRs) and their allosteric ligands. The understanding of how small …