Physics and Evolution of Biological Macromolecules
Disrupted chromatin architecture in olfactory sensory neurons: looking for the link from COVID-19 infection to anosmia
The COVID-19 pandemic, caused by the SARS-CoV-2 coronavirus, has placed significant strain on medical resources worldwide, and early detection and isolation has been the primary strategy by which, research establishments and governments worked to contain the disease spread.
ReadSequence-dependent model of allosteric communication
The omnipresence and diversity of allosteric regulation in proteins and protein associations complemented by the potential for the design of allosterically acting biologics and drugs call for the development of a new generation of computational models for the analysis of allostery and rational engineering/design of desired signaling and effector molecules determining it.
ReadAlloMAPS 2: allosteric fingerprints of the AlphaFold and Pfam-trRosetta predicted structures for engineering and design
AlloMAPS 2 is an update of the Allosteric Mutation Analysis and Polymorphism of Signalling database, which contains data on allosteric communication obtained for predicted structures in the AlphaFold database (AFDB) and trRosetta-predicted Pfam domains.
ReadMultiscale Allostery: Basic Mechanisms and Versatility in Diagnostics and Drug Design
There were several significant milestones in the last century, from the discovery of the Bohr effect to understanding that every dynamic protein is intrinsically allosteric
ReadAllosteric perspective on the mutability and druggability of the SARS-CoV-2 Spike protein
Keywords: SARS-CoV-2; Spike protein; allosteric drugs; allosteric effects of mutations; allostery; drug design; druggability; mutability.
ReadAllosteric perspective on the mutability and druggability of the SARS-CoV-2 Spike protein
Keywords: SARS-CoV-2; Spike protein; allosteric drugs; allosteric effects of mutations; allostery; drug design; druggability; mutability.
ReadDeriving and Using Descriptors of Elementary Functions in Rational Protein Design
The rational design of proteins with desired functions requires a comprehensive description of the functional building blocks. The evolutionary conserved functional units constitute nature's toolbox; however, they are not readily available to protein designers. This study focuses on protein units of subdomain size that possess structural properties and amino acid residues sufficient to carry out elementary reactions in the catalytic mechanisms.
ReadThree-dimensional Chromatin Ensemble Reconstruction via Stochastic Embedding
We propose a novel method for reconstructing the whole-genome chromatin ensemble from the Hi-C data. The procedure starts from the Markov State Modelling (MSM), delineating structural hierarchy of chromatin organization with partitioning and effective interactions archetypal for corresponding levels of hierarchy.
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