We review the history of the parallel tempering simulation method. From its origins in data
analysis, the parallel tempering method has become a standard workhorse of …

Artificial intelligence has made significant advances in the field of protein structure prediction
in recent years. In particular, DeepMind's end-to-end model, AlphaFold2, has demonstrated …

Protein secondary structure prediction began in 1951 when Pauling and Corey predicted
helical and sheet conformations for protein polypeptide backbone even before the first …

Molecular mechanics models have been applied extensively to study the dynamics of
proteins and nucleic acids. Here we report the development of a third-generation point …

RNA plays a crucial role not only in information transfer as messenger RNA during gene
expression but also in various biological functions as non-coding RNAs. Understanding …

Protein modeling could be done on various levels of structural details, from simplified lattice
or continuous representations, through high resolution reduced models, employing the …

Predicting a protein's structure from its amino acid sequence remains an unsolved problem
after several decades of efforts. If the query protein has a homolog of known structure, the …

We introduce a theoretical framework that exploits the ever-increasing genomic sequence
information for protein structure prediction. Structure-based models are modified to …

It is now almost 15 years since the publication of the first paper on text mining in the
genomics domain, and decades since the first paper on text mining in the medical domain …

Replica-exchange molecular dynamics simulations in implicit solvent have been carried out
to study the folding thermodynamics of a designed 20-residue peptide, or``miniprotein.''The …