Comparing proteins by their internal dynamics: Exploring structure–function relationships beyond static structural alignments
C Micheletti - Physics of life reviews, 2013 - Elsevier
The growing interest for comparing protein internal dynamics owes much to the realisation
that protein function can be accompanied or assisted by structural fluctuations and …
that protein function can be accompanied or assisted by structural fluctuations and …
[HTML][HTML] Comparing the intrinsic dynamics of multiple protein structures using elastic network models
Abstract Background Elastic network models (ENMs) are based on the simple idea that a
protein can be described as a set of particles connected by springs, which can then be used …
protein can be described as a set of particles connected by springs, which can then be used …
Measuring and comparing structural fluctuation patterns in large protein datasets
Motivation: The function of a protein depends not only on its structure but also on its
dynamics. This is at the basis of a large body of experimental and theoretical work on protein …
dynamics. This is at the basis of a large body of experimental and theoretical work on protein …
iPBA: a tool for protein structure comparison using sequence alignment strategies
JC Gelly, AP Joseph, N Srinivasan… - Nucleic acids …, 2011 - academic.oup.com
With the immense growth in the number of available protein structures, fast and accurate
structure comparison has been essential. We propose an efficient method for structure …
structure comparison has been essential. We propose an efficient method for structure …
Corresponding functional dynamics across the Hsp90 Chaperone family: insights from a multiscale analysis of MD simulations
Understanding how local protein modifications, such as binding small-molecule ligands, can
trigger and regulate large-scale motions of large protein domains is a major open issue in …
trigger and regulate large-scale motions of large protein domains is a major open issue in …
The structural asymmetry of mitochondrial Hsp90 (Trap1) determines fine tuning of functional dynamics
The Hsp90 family of molecular chaperones oversees the folding of a wide range of client
proteins. Hsp90 is a homodimer, whose conformational states and functions are regulated …
proteins. Hsp90 is a homodimer, whose conformational states and functions are regulated …
Algorithms, applications, and challenges of protein structure alignment
As a fundamental problem in computational structure biology, protein structure alignment
has attracted the focus of the community for more than 20 years. While the pairwise structure …
has attracted the focus of the community for more than 20 years. While the pairwise structure …
Computational approaches elucidate the allosteric mechanism of human aromatase inhibition: a novel possible route to Small-molecule regulation of CYP450s …
Human aromatase (HA) is a P450 cytochrome (CYP) with an essential role in estrogen
biosynthesis. Since more than 70% of breast cancers are positive for estrogenic receptor …
biosynthesis. Since more than 70% of breast cancers are positive for estrogenic receptor …
Network-based models as tools hinting at nonevident protein functionality
Network-based models of proteins are popular tools employed to determine dynamic
features related to the folded structure. They encompass all topological and geometric …
features related to the folded structure. They encompass all topological and geometric …
Information-theoretical measures identify accurate low-resolution representations of protein configurational space
The steadily growing computational power employed to perform molecular dynamics
simulations of biological macromolecules represents at the same time an immense …
simulations of biological macromolecules represents at the same time an immense …