DBAli: a database of protein structure alignments. - Marc A. Martí-Renom; Valentin A. Ilyin; Andrej Sali (Bioinform., 2001)

LigBase: a database of families of aligned ligand binding sites in known protein sequences and structures. - Ashley C. Stuart; Valentin A. Ilyin; Andrej Sali (Bioinform., 2002)

MODBASE, a database of annotated comparative protein structure models. - Ursula Pieper 001; Narayanan Eswar; Ashley C. Stuart; Valentin A. Ilyin; Andrej Sali (Nucleic Acids Res., 2002)

ModView, visualization of multiple protein sequences and structures. - Valentin A. Ilyin; Ursula Pieper 001; Ashley C. Stuart; Marc A. Martí-Renom; Linda McMahan; Andrej Sali (Bioinform., 2003)

Tools for comparative protein structure modeling and analysis. - Narayanan Eswar; Bino John; Nebojsa Mirkovic; András Fiser; Valentin A. Ilyin; Ursula Pieper 001; Ashley C. Stuart; Marc A. Martí-Renom; Mallur S. Madhusudhan; Bozidar Yerkovich; Andrej Sali (Nucleic Acids Res., 2003)

THEMATICS is Effective for Active Site Prediction in Comparative Model Structures. - Ihsan A. Shehadi; Alper Uzun; Leonel F. Murga; Valentin A. Ilyin; Mary Jo Ondrechen (APBC, 2004)

Structural exon database, SEDB, mapping exon boundaries on multiple protein structures. - Chesley M. Leslin; Alexej Abyzov; Valentin A. Ilyin (Bioinform., 2004)

Friend, an integrated analytical front-end application for bioinformatics. - Alexej Abyzov; Mounir Errami; Chesley M. Leslin; Valentin A. Ilyin (Bioinform., 2005)

Active Site Prediction for Comparative Model Structures with Thematics. - Ihsan A. Shehadi; Alexej Abyzov; Alper Uzun; Ying Wei; Leonel F. Murga; Valentin A. Ilyin; Mary Jo Ondrechen (J. Bioinform. Comput. Biol., 2005)

TOPOFIT-DB, a database of protein structural alignments based on the TOPOFIT method. - Chesley M. Leslin; Alexej Abyzov; Valentin A. Ilyin (Nucleic Acids Res., 2007)

Structure SNP (StSNP): a web server for mapping and modeling nsSNPs on protein structures with linkage to metabolic pathways. - Alper Uzun; Chesley M. Leslin; Alexej Abyzov; Valentin A. Ilyin (Nucleic Acids Res., 2007)

An AP Endonuclease 1-DNA Polymerase β Complex: Theoretical Prediction of Interacting Surfaces. - Alexej Abyzov; Alper Uzun; Phyllis R. Strauss; Valentin A. Ilyin (PLoS Comput. Biol., 2008)