Abyzov A, Uzun A, Strauss PR, Ilyin VA. An AP endonuclease 1 - DNA polymerase &beta complex: Theoretical prediction of interacting surfaces. Submitted.
Godoy VG, Jarosz DF, Simon SM, Abyzov A, Ilyin VA, Walker GC. UmuD and RecA Directly Modulate the Mutagenic Potential of the Y-family DNA Polymerase DinB. Molecular Cell. 2007 (in press)
Abyzov A, Ilyin VA. A comprehensive analysis of non-sequential alignments between all protein structures. BMC Structural Biology 2007, 7:78.
Stoeck T, Kasper J, Bunge J, Leslin C, Ilyin V, Epstein S. Protistan diversity in the arctic: a case of paleoclimate shaping modern biodiversity? PLoS ONE. 2007 Aug 15;2(1):e728.
Uzun A, Leslin CM, Abyzov A, Ilyin V. Structure SNP (StSNP): a web server for mapping and modeling nsSNPs on protein structures with linkage to metabolic pathways. Nucleic Acids Res. 2007 Jul 1;35:W384-92.
Shehadi IA, Abyzov A, Uzun A, Wei Y, Murga LF, Ilyin V, Ondrechen MJ. Active Site Prediction for Comparative Model Structures with THEMATICS. J Bioinform Comput Biol. 2005 Feb;3(1):127-43.
Ilyin VA, Abyzov A, Leslin CM. Structural alignment of proteins by a novel TOPOFIT method, as a
superimposition of common volumes at a topomax point. Protein Sci. 2004 Jul;13(7):1865-74.
Eswar N, John B, Mirkovic N, Fiser A, Ilyin VA, Pieper U, Stuart AC, Marti-Renom MA, Madhusudhan MS, Yerkovich B, Sali A. Tools for comparative protein structure modeling and analysis. Nucleic Acids Res. 2003 Jul 1;31(13):3375-80.
Ilyin VA, Pieper U, Stuart AC, Marti-Renom MA, McMahan L, Sali A. ModView, visualization of multiple protein sequences and structures. Bioinformatics. 2003 Jan;19(1):165-6.
Retailleau P, Huang X, Yin Y, Hu M, Weinreb V, Vachette P, Vonrhein C, Bricogne G, Roversi P, Ilyin V, Carter CW Jr. Interconversion of ATP binding and conformational free energies by tryptophanyl-tRNA synthetase: structures of ATP bound to open and closed, pre-transition-state conformations. J Mol Biol. 2003 Jan 3;325(1):39-63.
Chance MR, Bresnick AR, Burley SK, Jiang JS, Lima CD, Sali A, Almo SC, Bonanno JB, Buglino JA, Boulton S, Chen H, Eswar N, He G, Huang R, Ilyin V, McMahan L, Pieper U, Ray S, Vidal M, Wang LK. High throughput structural biology: A pipeline for providing structures for the biologist. Protein Sci 2002 Apr;11(4):723-38.
Bonanno JB, Edo C, Eswar N, Pieper U, Romanowski MJ, Ilyin V, Gerchman SE, Kycia H, Studier FW, Sali A, Burley SK. Structural genomics of enzymes involved in sterol/isoprenoid biosynthesis. Proc Natl Acad Sci U S A 2001 Nov 6;98(23):12896-901.
Ilyin VA, Temple B, Hu M, Li G, Yin Y, Vachette P, Carter CW Jr. 2.9 A crystal structure of ligand-free tryptophanyl-tRNA synthetase: domain movements fragment the adenine nucleotide binding site. Protein Sci. 2000 Feb;9(2):218-31.
Carter CW, Retailleau P, Ilyin V, Huang X, Yin Y, Vachette P. Trp-tRNA synthetase three-state behavior resembles that of motor proteins. BIOPHYSICAL JOURNAL 78 (1): 852Plat, Part 2 JAN 2000.
Carter CW Jr, Ilyin V, Huang X, Yin Y, Retailleau P, Vachette P, Longo A, Hu M. (1999). Acta Cryst. A55 Suppl., 05.04.009.
Ilyin V, Carter CW Jr. Protein coordinates in Protein Data Bank 1D2R
(Tryptophanyl-tRNA synthetase), 1999.
Ilyin VA. Protein Homology. First Workshop on Computational Biology. CSHL, NY, September 7 - 9, 1999.
Carter CW, Ilyin VA, Huang X, Yin Y, Reatailleau P, Vachette P, Longo A, Hu M. TrpRS: Three-State Behaviour, Induced fit, conformational Coupling, and free energy trunsdaction. P05.04.009; XVIII IUCr Congress, Glasgow, Scotland. Aug 1999.
Ilyin VA. A New Approach to Protein Structure Alignment. Cold Spring Harbor Laboratory. Bioinformatics Seminar. May 14, 1999.
Ilyin VA, Xinag Z., Carter CW Jr. 2.5 A Crystal Structure of Trp complex of Tryptophanol tRNA synthetase. 1998, ACA-98, Washington.
Ilyin VA, Carter CW Jr, Winborne E, Temple B, Li G. 2.9 CRYSTAL STRUCTURE OF LIGAND-FREE TRYPTOPHANYL-TRNA SYNTHETASE. 1996, IUCr 96, Seatle.
Ilyin V.A. Structures of hydrophobic cores in proteins. Symposium on Distance-Based Approaches to Protein Structure Determination II, Copenhaven, Denmark, Nov. 1994.
Kolbanovskaia EI, Morozov NI, Gavriushov SA, Il'in VA, Beintmena J, Vlodaver A, Karpeiskii MI. [Structure-activity analysis of ribonuclease A and related proteins]. Mol Biol (Mosk). 1993 Nov-Dec;27(6):1315-34.
Kolbanovskaya E.Yu., Ilyin V.A., Karpeisky M.Ya., Beintema J.J., Wlodaver A. Comparative analysis of nonpolar regions in cyclizing ribonucleases. 3th International Meeting. Ribonucleases: Chemistry, Biology, Biotechnology. 1993, Italy.
Karpeisky M.Ya., Ilyin V.A., Sevcik J. Non-polar interactions in RNases Pb1, Sa, Bi. Metabolism and Enzimology of Nucleic Acids Including Gene Manipulations (Zelinka, J. & Balan, J. eds., Bratislava), 1991, v.7, p. 265-275.
