Tailor-made multiple sequence alignments using the PRALINE 2 alignment toolkit

SUMMARY: PRALINE 2 is a toolkit for custom multiple sequence alignment workflows. It can be used to incorporate sequence annotations, such as secondary structure or (DNA) motifs, into the alignment scoring, as well as to customize many other aspects of a progressive multiple alignment workflow. AVAILABILITY AND IMPLEMENTATION: PRALINE 2 is implemented in Python and available as open source software on GitHub: https://github.com/ibivu/PRALINE/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online

A repertoire of representative Val60 structures generated using the CamTube force field.

<p>A selection of 135 structures whose TM-score from respective CATH structures is larger than 0.4; a-c) examples of three CATH structures with their equivalent Val60 structures. CATH codes are given bellow the respective figures.</p

Atom pair self-avoiding sphere distances, <i>d</i>, from Eq 1.

<p>Atom pair self-avoiding sphere distances, <i>d</i>, from <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004435#pcbi.1004435.e001" target="_blank">Eq 1</a>.</p

Free energy surface of Val60 in the CamTube force field.

<p>The x and y axes represent two CV variables: the number of α-helical six-residue-long fragments and the radius of gyration.</p

Schematic representation of a segment of a polypeptide chain in the CamTube model.

<p>The tube-like implementation is carried out by self-avoiding spheres, which for clarity of illustration are shown here only for Cα atoms. Bond lengths (apart from the Cα-Cβ bond) and angles are taken from the Amber force field. The length of the CA-Cβ bond of Val, Pro, Thr, Ser and Cys is scaled 1.5 times; Asp, Ile, Leu and Asn 2 times; Phe 2.25 times; Glu, Gln, Met and His 2.5 times; Tyr and Trp 3 times; Lys and Arg 4 times the length of the Cα-Cβ bond in the Amber force field.</p

Parameters for Cβ-Cα-N-C' and Cβ-Cα-C'-N dihedral angles used in the CamTube force field that encode the propensity of the amino acids for different regions in the Ramachandran map.

<p>Parameters for Cβ-Cα-N-C' and Cβ-Cα-C'-N dihedral angles used in the CamTube force field that encode the propensity of the amino acids for different regions in the Ramachandran map.</p

Illustration of the repulsion between C' and H atoms introduced by the curvature term in the CamTube model.

<p>The C' and H atoms belong to the α-helix and are 2 and 3 residues apart in the sequence.</p