AlphaFold, artificial intelligence (AI), and allostery
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 …
Machine learning force fields and coarse-grained variables in molecular dynamics: application to materials and biological systems
Machine learning encompasses tools and algorithms that are now becoming popular in
almost all scientific and technological fields. This is true for molecular dynamics as well …
almost all scientific and technological fields. This is true for molecular dynamics as well …
PED in 2021: a major update of the protein ensemble database for intrinsically disordered proteins
Abstract The Protein Ensemble Database (PED)(https://proteinensemble. org), which holds
structural ensembles of intrinsically disordered proteins (IDPs), has been significantly …
structural ensembles of intrinsically disordered proteins (IDPs), has been significantly …
Advances in molecular dynamics simulations and enhanced sampling methods for the study of protein systems
Molecular dynamics (MD) simulation is a rigorous theoretical tool that when used efficiently
could provide reliable answers to questions pertaining to the structure-function relationship …
could provide reliable answers to questions pertaining to the structure-function relationship …
De novo design of allosterically switchable protein assemblies
Allosteric modulation of protein function, wherein the binding of an effector to a protein
triggers conformational changes at distant functional sites, plays a central part in the control …
triggers conformational changes at distant functional sites, plays a central part in the control …
Critical assessment of methods for predicting the 3D structure of proteins and protein complexes
Advances in a scientific discipline are often measured by small, incremental steps. In this
review, we report on two intertwined disciplines in the protein structure prediction field …
review, we report on two intertwined disciplines in the protein structure prediction field …
Discovery of cryptic allosteric sites using reversed allosteric communication by a combined computational and experimental strategy
Allostery, which is one of the most direct and efficient methods to fine-tune protein functions,
has gained increasing recognition in drug discovery. However, there are several challenges …
has gained increasing recognition in drug discovery. However, there are several challenges …
Emerging roles of SIRT6 in human diseases and its modulators
The biological functions of sirtuin 6 (SIRT6; eg, deacetylation, defatty‐acylation, and mono‐
ADP‐ribosylation) play a pivotal role in regulating lifespan and several fundamental …
ADP‐ribosylation) play a pivotal role in regulating lifespan and several fundamental …
PASSer: fast and accurate prediction of protein allosteric sites
Allostery refers to the biological process by which an effector modulator binds to a protein at
a site distant from the active site, known as allosteric site. Identifying allosteric sites is …
a site distant from the active site, known as allosteric site. Identifying allosteric sites is …
The role of conformational dynamics and allostery in modulating protein evolution
Advances in sequencing techniques and statistical methods have made it possible not only
to predict sequences of ancestral proteins but also to identify thousands of mutations in the …
to predict sequences of ancestral proteins but also to identify thousands of mutations in the …