RELIC--a bioinformatics server for combinatorial peptide analysis and identification of protein-ligand interaction sites.
Phage display technology provides a versatile tool for exploring the interactions between proteins, peptides and small molecule ligands. Quantitative analysis of peptide population sequence diversity and bias patterns has the power to significantly enhance the impact of these methods [1, 2]. We have developed a suite of computational tools for the analysis of peptide populations and made them accessible by integrating fifteen software programs for the analysis of combinatorial peptide sequences into the REceptor LIgand Contacts (RELIC) relational database and web-server. These programs have been developed for the analysis of statistical properties of peptide populations; identification of weak consensus sequences within these populations; and the comparison of these peptide sequences to those of naturally occurring proteins. RELIC is particularly suited to the analysis of peptide populations affinity selected with a small molecule ligand such as a drug or metabolite. Within this functional context, the ability to identify potential small molecule binding proteins using combinatorial peptide screening will accelerate as more ligands are screened and more genome sequences become available. The broader impact of this work is the addition of a novel means of analyzing peptide populations to the phage display community.
Mandava
Suneeta
S
Biociences Division, Argonne National Laboratory, Argonne, IL 60439, USA.
Makowski
Lee
L
Devarapalli
Satish
S
Uzubell
Joseph
J
Rodi
Diane J
DJ
D000465:Algorithms; D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D020650:Combinatorial Chemistry Techniques / Q000379:methods*; D019295:Computational Biology; D020407:Internet; D008024:Ligands; D008958:Models, Molecular; D008969:Molecular Sequence Data; D019151:Peptide Library; D010455:Peptides / Q000032:analysis*; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D011994:Recombinant Proteins / Q000737:chemistry; D017422:Sequence Analysis, DNA; D017386:Sequence Homology, Amino Acid; D012984:Software
D008024:Ligands; D019151:Peptide Library; D010455:Peptides; D011506:Proteins; D011994:Recombinant Proteins