Tan ZW
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.
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.
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.
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.
ReadAlloSigMA 2: paving the way to designing allosteric effectors and to exploring allosteric effects of mutations
The AlloSigMA 2 server provides an interactive platform for exploring the allosteric signaling caused by ligand binding and/or mutations, for analyzing the allosteric effects of mutations and for detecting potential cancer drivers and pathogenic nsSNPs. It can also be used for searching latent allosteric sites and for computationally designing allosteric effectors for these sites with required agonist/antagonist activity.
ReadExploring chromatin hierarchical organization via Markov State Modelling
We propose a new computational method for exploring chromatin structural organization based on Markov State Modelling of Hi-C data represented as an interaction network between genomic loci. A Markov process describes the random walk of a traveling probe in the corresponding energy landscape, mimicking the motion of a biomolecule involved in chromatin function. By studying the metastability of the associated Markov State Model upon annealing, the hierarchical structure of individual chromosomes is observed, and corresponding set of structural partitions is identified at each level of hierarchy.
ReadAlloMAPS: allosteric mutation analysis and polymorphism of signaling database
AlloMAPS database provides data on the causality and energetics of allosteric communication obtained with the structure-based statistical mechanical model of allostery (SBSMMA). The database contains data on allosteric signaling in three sets of proteins and protein chains: (i) 46 proteins with comprehensively annotated functional and allosteric sites; (ii) 1908 protein chains from PDBselect set of chains with low (<25%) sequence identity; (iii) 33 proteins with more than 50 known pathological SNPs in each molecule.
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