1. A. A. Podtelezhnikov and D. L. Wild. CRANKITE – A Fast Polypeptide Backbone Conformation Sampler, submitted to Bioinformatics (2007).
  2. A. A. Podtelezhnikov, N. T. Amin, R. B. Freedman, D. L. Wild. Reconstruction of All-Atom Protein Backbone Conformation from Regularized Contact Maps, submitted to Proteins (2007).
  3. A. A. Podtelezhnikov, Z. Ghahramani, D. L. Wild. Learning about protein hydrogen bonding by minimizing contrastive divergence, Proteins 66, 588-599 (2007). Abstract
  4. W. Chu, Z. Ghahramani, A. Podtelezhnikov, D. L. Wild. Bayesian segmental models with multiple sequence alignment profiles for protein secondary structure and contact map prediction, IEEE/ACM Trans. Comp. Biol. Bioinformatics 3, 98-113 (2006). Abstract
  5. A. A. Podtelezhnikov and D. L. Wild. Exhaustive Metropolis Monte Carlo sampling and analysis of polyalanine conformations adopted under the influence of hydrogen bonds, Proteins 61, 94-104 (2005). Abstract
  6. A. A. Podtelezhnikov, K. Gao, F. D. Bushman and J. A. McCammon. Modeling HIV-1 integrase complexes based on their hydrodynamic properties, Biopolymers 68, 110-120 (2003). Abstract
  7. A. V. Vologodskii, W. T. Zhang, V. V. Rybenkov, A. A. Podtelezhnikov, D. Subramanian, J. D. Griffith, N. R. Cozzarelli. Mechanism of topology simplification by type II DNA topoisomerases, Proc. Natl. Acad. Sci. U.S.A. 98, 3045-3049 (2001). Abstract
  8. A. A. Podtelezhnikov, C. Mao, N. C. Seeman and A. V. Vologodskii. Multimerization-cyclization of DNA fragments as a method of conformational analysis, Biophysical Journal 79, 2692-2704 (2000). Abstract
  9. A. A. Podtelezhnikov and A. V. Vologodskii. Dynamics of small loops in DNA molecules, Macromolecules 33, 2767-2771 (2000). Abstract
  10. A. A. Podtelezhnikov, N. R. Cozzarelli and A. V. Vologodskii. Equilibrium distributions of topological states in circular DNA: interplay of supercoiling and knotting, Proc. Natl. Acad. Sci. U.S.A. 96, 12974-12979 (1999). Abstract
  11. A. S. Krasilnikov, A. Podtelezhnikov, A. Vologodskii and S. M. Mirkin. Large-scale effects of transcriptional DNA supercoiling in vivo, J. Mol. Biol. 292, 1149-1160 (1999). Abstract
  12. A. A. Podtelezhnikov and A. V. Vologodskii. Simulations of polymer cyclization by Brownian Dynamics, Macromolecules 30, 6668-6673 (1997). Abstract
  13. A. A. Podtelezhnikov, A. V. Kurakin, A. V. Vologodskii and D. I. Cherny. Testing the quality of electron microscope mapping data for DNA molecules with sequence-specific ligands, Micron 25, 439-446 (1994). Abstract