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Principal components analysis: a review of its application on molecular dynamics data
SAM Stein, AE Loccisano, SM Firestine… - Annual Reports in …, 2006 - Elsevier
Publisher Summary This chapter discusses the need for multivariate analysis in biophysical
studies, presents the way principal components analysis (PCA) can be implemented in the …
studies, presents the way principal components analysis (PCA) can be implemented in the …
Alpha shape and Delaunay triangulation in studies of protein-related interactions
In recent years, more 3D protein structures have become available, which has made the
analysis of large molecular structures much easier. There is a strong demand for geometric …
analysis of large molecular structures much easier. There is a strong demand for geometric …
Discrimination of thermophilic and mesophilic proteins
TJ Taylor, II Vaisman - BMC structural biology, 2010 - Springer
Background There is a considerable literature on the source of the thermostability of proteins
from thermophilic organisms. Understanding the mechanisms for this thermostability would …
from thermophilic organisms. Understanding the mechanisms for this thermostability would …
Alternative splicing and protein structure evolution
Alternative splicing is thought to be one of the major sources for functional diversity in higher
eukaryotes. Interestingly, when map** splicing events onto protein structures, about half of …
eukaryotes. Interestingly, when map** splicing events onto protein structures, about half of …
Multiscale modeling of nucleosome dynamics
Nucleosomes form the fundamental building blocks of chromatin. Subtle modifications of the
constituent histone tails mediate chromatin stability and regulate gene expression. For this …
constituent histone tails mediate chromatin stability and regulate gene expression. For this …
A minimal TrpRS catalytic domain supports sense/antisense ancestry of class I and II aminoacyl-tRNA synthetases
The emergence of polypeptide catalysts for amino acid activation, the slowest step in protein
synthesis, poses a significant puzzle associated with the origin of biology. This problem is …
synthesis, poses a significant puzzle associated with the origin of biology. This problem is …
The Rodin-Ohno hypothesis that two enzyme superfamilies descended from one ancestral gene: an unlikely scenario for the origins of translation that will not be …
CW Carter, L Li, V Weinreb, M Collier… - Biology Direct, 2014 - Springer
Background Because amino acid activation is rate-limiting for uncatalyzed protein synthesis,
it is a key puzzle in understanding the origin of the genetic code. Two unrelated classes (I …
it is a key puzzle in understanding the origin of the genetic code. Two unrelated classes (I …
Multidimensional phylogenetic metrics identify class I aminoacyl-tRNA synthetase evolutionary mosaicity and inter-modular coupling
The role of aminoacyl-tRNA synthetases (aaRS) in the emergence and evolution of genetic
coding poses challenging questions concerning their provenance. We seek evidence about …
coding poses challenging questions concerning their provenance. We seek evidence about …
Vorolign—fast structural alignment using Voronoi contacts
Vorolign, a fast and flexible structural alignment method for two or more protein structures is
introduced. The method aligns protein structures using double dynamic programming and …
introduced. The method aligns protein structures using double dynamic programming and …
Base pairing promoted the self-organization of genetic coding, catalysis, and free-energy transduction
CW Carter Jr - Life, 2024 - mdpi.com
How Nature discovered genetic coding is a largely ignored question, yet the answer is key to
explaining the transition from biochemical building blocks to life. Other, related puzzles also …
explaining the transition from biochemical building blocks to life. Other, related puzzles also …