▪ Abstract Comparative modeling predicts the three-dimensional structure of a given protein
sequence (target) based primarily on its alignment to one or more proteins of known …

Almost all protein database search methods use amino acid substitution matrices for
scoring, optimizing, and assessing the statistical significance of sequence alignments. Much …

We are at the beginning of a genomic revolution in which all known species are planned to
be sequenced. Accessing such data for comparative analyses is crucial in this new age of …

Protein modeling is an increasingly popular area of machine learning research. Semi-
supervised learning has emerged as an important paradigm in protein modeling due to the …

Comparative protein structure modeling predicts the three‐dimensional structure of a given
protein sequence (target) based primarily on its alignment to one or more proteins of known …

The idea for this book came from the time the authors spent at the Statistics and Applied
Mathematical Sciences Institute (SAMSI) in Research Triangle Park in North Carolina …

Sequence alignments unambiguously distinguish between protein pairs of similar and non-
similar structure when the pairwise sequence identity is high (> 40% for long alignments) …

Abstract Background Profile hidden Markov models (profile-HMMs) are sensitive tools for
remote protein homology detection, but the main scoring algorithms, Viterbi or Forward …

Of the sequence comparison methods, profile-based methods perform with greater
selectively than those that use pairwise comparisons. Of the profile methods, hidden Markov …

The BLAST algorithm was developed as a way to perform DNA and protein sequence
similarity searches by an algorithm that is faster than FASTA but considered to be equally as …