@inbook{36cf5e7ced76465291cbe0bd3cae0ebb,
title = "PROMALS3D: Multiple protein sequence alignment enhanced with evolutionary and three-dimensional structural information",
abstract = "Multiple sequence alignment (MSA) is an essential tool with many applications in bioinformatics and computational biology. Accurate MSA construction for divergent proteins remains a difficult computational task. The constantly increasing protein sequences and structures in public databases could be used to improve alignment quality. PROMALS3D is a tool for protein MSA construction enhanced with additional evolutionary and structural information from database searches. PROMALS3D automatically identifies homologs from sequence and structure databases for input proteins, derives structure-based constraints from alignments of three-dimensional structures, and combines them with sequence-based constraints of profile-profile alignments in a consistency-based framework to construct high-quality multiple sequence alignments. PROMALS3D output is a consensus alignment enriched with sequence and structural information about input proteins and their homologs. PROMALS3D Web server and package are available at http://prodata.swmed.edu/PROMALS3D.",
keywords = "Consistency-based scoring, Database searches, Multiple sequence alignment, Probabilistic model of profile-profile alignment, Three-dimensional structural alignment",
author = "Jimin Pei and Grishin, {Nick V.}",
year = "2014",
doi = "10.1007/978-1-62703-646-7-17",
language = "English (US)",
isbn = "9781627036450",
volume = "1079",
series = "Methods in Molecular Biology",
pages = "263--271",
booktitle = "Methods in Molecular Biology",
}