3DCoffee: combining protein sequences and structures within multiple sequence alignments.

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COBALT: constraint-based alignment tool for multiple protein sequences (2007, background): “Even the latter primarily restrict themselves to observations of the input dataset, for example, the secondary structure locations on the inputs (O’Sullivan et al ., 2004).”
Cloud-Coffee: implementation of a parallel consistency-based multiple alignment algorithm in the T-Coffee package and its benchmarking on the Amazon Elastic-Cloud (2010, methodology): “Availability: T-Coffee is a freeware open source package available from http://www.tcoffee.org/homepage.html Contact: cedric.notredame@crg.es Received on March 30, 2010; revised on May 18, 2010; accepted on June 2, 2010”
MAFFT version 5: improvement in accuracy of multiple sequence alignment (2005, methodology): “An up-to-date version of HOM39 (26) was extracted from the July 2004 release of HOMSTRAD (17) (http://www-cryst.”
MAFFT-DASH: integrated protein sequence and structural alignment (2019, background): “An established approach for improving protein MSA accuracy, which was first introduced in 3DCoffee (6), is to incorporate tertiary structural information.”
Residue centrality, functionally important residues, and active site shape: Analysis of enzyme and non‐enzyme families (2006, background): “Here, et al. 2004 we aimed to study the generality of this result by analyzing a set of biologically different protein families, involving different functionally important sites.”