Protein Block Expert (PBE): a web-based protein structure analysis server using a structural alphabet. - Manoj Tyagi; P. Sharma; C. S. Swamy; F. Cadet; Narayanaswamy Srinivasan; Alexandre G. de Brevern; Bernard O. Offmann (Nucleic Acids Res., 2006)

Protein short loop prediction in terms of a structural alphabet. - Manoj Tyagi; Aurélie Bornot; Bernard O. Offmann; Alexandre G. de Brevern (Comput. Biol. Chem., 2009)

Knowledge-based annotation of small molecule binding sites in proteins. - Ratna R. Thangudu; Manoj Tyagi; Benjamin A. Shoemaker; Stephen H. Bryant; Anna R. Panchenko; Thomas Madej (BMC Bioinform., 2010)

Inferred Biomolecular Interaction Server - a web server to analyze and predict protein interacting partners and binding sites. - Benjamin A. Shoemaker; Dachuan Zhang; Ratna R. Thangudu; Manoj Tyagi; Jessica H. Fong; Aron Marchler-Bauer; Stephen H. Bryant; Tom Madej; Anna R. Panchenko (Nucleic Acids Res., 2010)

IBIS (Inferred Biomolecular Interaction Server) reports, predicts and integrates multiple types of conserved interactions for proteins. - Benjamin A. Shoemaker; Dachuan Zhang; Manoj Tyagi; Ratna R. Thangudu; Jessica H. Fong; Aron Marchler-Bauer; Stephen H. Bryant; Thomas Madej; Anna R. Panchenko (Nucleic Acids Res., 2012)