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 …

Alpha shape and Delaunay triangulation in studies of protein-related interactions

W Zhou, H Yan - Briefings in bioinformatics, 2014 - academic.oup.com
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 …

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 …

Alternative splicing and protein structure evolution

F Birzele, G Csaba, R Zimmer - Nucleic acids research, 2008 - academic.oup.com
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 …

Multiscale modeling of nucleosome dynamics

S Sharma, F Ding, NV Dokholyan - Biophysical journal, 2007 - cell.com
Nucleosomes form the fundamental building blocks of chromatin. Subtle modifications of the
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

Y Pham, L Li, A Kim, O Erdogan, V Weinreb… - Molecular cell, 2007 - cell.com
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 …

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 …

Multidimensional phylogenetic metrics identify class I aminoacyl-tRNA synthetase evolutionary mosaicity and inter-modular coupling

CW Carter Jr, A Po**a, R Bouckaert… - International Journal of …, 2022 - mdpi.com
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 …

Vorolign—fast structural alignment using Voronoi contacts

F Birzele, JE Gewehr, G Csaba, R Zimmer - Bioinformatics, 2007 - academic.oup.com
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 …

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 …