In the longer term, and combined with an atomic-level analysis of epitope specificity, some of these mAbs may facilitate the templatebased design of immunogens for the development of a vaccine able to induce neutralizing antibodies against the wide range of HIV-1 strains present in the global pandemic. Figure S1 Binding of gp120 and gp41-specific mAbs to a panel of 15 recombinant Env proteins from different clades. Found at: doi:10.1371/journal.pone.0008805.s001 (0.47 MB PDF) Figure 6 . Epitope specificity and neutralizing activity of the mAb panel. The pie chart shows the specificity of the 58 mAbs isolated from the 21 interrogated individuals. The fraction of antibodies with neutralizing activity against at least one isolate is indicated in parentheses. Partial CD4bs, incomplete inhibition of CD4 binding; HR-1/ FP, epitope located in between HR-1 and the fusion peptide as determined by 5F3 competition; HR-1/5HB, recognition of trimeric HR-1 and 5-helix bundle; 5HB, 5 helix bundle; C-C region, gp41 immunodominant region; HR-2, heptad-repeat 2; ND, not defined epitopes within gp120 or gp41. doi:10.1371/journal.pone.0008805.g006 Recode-2: new design, new search tools, and many more genes ‘Recoding’ is a term used to describe non-standard read-out of the genetic code, and encompasses such phenomena as programmed ribosomal frameshifting, stop codon readthrough, selenocysteine insertion and translational bypassing. Although only a small proportion of genes utilize recoding in protein synthesis, accurate annotation of ‘recoded’ genes lags far behind annotation of ‘standard’ genes. In order to address this issue, provide a service to researchers in the field, and offer training data for developers of gene-annotation software, we have gathered together known cases of recoding within the Recode database. Recode-2 is an improved and updated version of the database. It provides access to detailed information on genes known to utilize translational recoding and allows complex search queries, browsing of recoding data and enhanced visualization of annotated sequence elements. At present, the Recode-2 database stores information on approximately 1500 genes that are known to utilize recoding in their expression—a factor of approximately three increase over the previous version of the database. Recode-2 is available at http://recode.ucc.ie The term 'translational recoding' describes the utilization of non-standard decoding during protein synthesis and encompasses such processes as ribosomal frameshifting, codon redefinition, translational bypassing and StopGo (1) (2) (3) (4) (5) (6) (7) . What is often considered as a decoding error-e.g. a frameshifting error or mistranslation of a particular codon-may occasionally benefit the organism by increasing its fitness and survival. In such instances the propensity for the decoding 'error' may be selected for during evolution, leading to the formation of a particular sequence context that elevates the frequency of the 'error'. To discriminate such cases of programmed decoding 'misbehaviour' from promiscuous translational errors or translational noise, the term recoding is used. The position within an mRNA where a recoding event takes place is termed the 'recoding site'. Sequence elements responsible for increasing the efficiency of recoding events are termed 'recoding stimulatory signals', and a minimal sequence fragment that allows recoding to take place at the natural efficiency (i.e. relative to the level of standard decoding at the recoding site) is termed a 'recoding cassette'.