Predicted coevolving pairs between amino acids located in V3 and other structural regions of HIV-1 Env.

<p>Gp120 is shown in cartoon representation, with V1 coloured in blue, V2 in pink and V3 in orange. (A) All inter V3 coevolving pairs are highlighted with green (TP) or red (FP) coloured dashes. (B) Coevolving amino acid pairs Glu293-Asn295, Glu293-Thr297, His330-Asn332 and His330-Ser334 (shown in sticks representation) are mediated by N-linked glycans (shown as black lines). (C) Predicted contacts between amino acids located in V1V2 and V3. The involved amino acids are highlighted as coloured sticks.</p

Coevolution network of the inter gp120-gp41 coevolving pair Pro238-Glu630.

<p>This pair may affect the gp120-gp41 interaction, although their are not proximal, through their intra-domain coevolving residue partners.</p

Predicted coevolving residue pairs within V3.

<p>TP predicted coevolving pairs are connected with a green dash and the FP ones are shown as red bonds. Amino acid numbering is according the HXB2 reference sequence and the V3 coordinate structure solved by Huang et al. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0143245#pone.0143245.ref011" target="_blank">11</a>] is applied for visualisation. (A) Travers and co-authors [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0143245#pone.0143245.ref042" target="_blank">42</a>] identified 24 coevolving pairs of which the majority is FP. (B) Coevolution predictions made by GREMLIN identified almost exclusively TP.</p

Coevolving pairs between amino acids in V1V2 and other structural HIV-1 Env domains.

<p>V1, V2 and V3 are shown in skyblue, pink and orange coloured cartoon illustration. (A) 59 predicted and in [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0143245#pone.0143245.ref049" target="_blank">49</a>] crystallised coevolving residue pairs; with TP illustrated as green and FP as red dashes. (B) Two long-distance coevolving amino acids are quite likely mediated by a N-linked glycan. The involved amino acids are shown in stick representation. (C) Three long-distance residue pairs (Ile165-Lys192, Gly167-Lys192, and Gly167-Met426) are presumably inter gp120 contacts. The intra- and inter-gp120 distances are shown as coloured (orange,light green and yellow) bonds. The inter-gp120 distances are in all cases smaller than the intra-gp120 ones.</p

HIV cell entry.

<p>Schematic illustration of HIV-1 entry steps attachment and coreceptor binding.</p

Additional file 3 of COUSCOus: improved protein contact prediction using an empirical Bayes covariance estimator

Scatterplot comparing the accuracies of the top L contacts of PSICOV to COUSCOus, using sequence separation ≥6. (PDF 78 kb

Additional file 2 of COUSCOus: improved protein contact prediction using an empirical Bayes covariance estimator

Mean accuracies of several contact detecting methods for the top- L/10,L/5 and L predictions for all contact types applying the PSICOV benchmark dataset. (PDF 85.6 kb