Conformational Studies of Polypeptides

This project is carried in collaboration with H. A. Scheraga and members of his group at the Department of Chemistry at Cornell.


“Folding of the Villin Headpiece Subdomain from Random Structures. Analysis of the Charge Distribution as a Function of the pH.” D.R. Ripoll, J.A. Vila and H.A. Scheraga. (2004). J. Mol. Biol. 339, 915-925. [pdf]






 “Atomically detailed folding simulation of the B domain of staphylococcal protein A from random structures.”   J.A. Vila, D.R. Ripoll, and H.A. Scheraga. (2003).  Proc. Natl Acad. Sci. USA. 100, 14812-14816.[pdf]





  A. Liwo, J. Lee, D.R. Ripoll, J. Pillardy, and H.A. Scheraga. (1999). “Protein Structure Prediction by Global Optimization of a Potential Energy Function”. Proc. Natl. Acad. Sci. USA, 96, 5482-5485. [pdf]

  J. Lee, A. Liwo, D.R. Ripoll, J. Pillardy and H.A. Scheraga. (1999). “Calculation of Protein Conformation by Global Optimization of a Potential Energy Function”. Proteins Struct. Funct. Genet. Suppl. 3, 204-208. [pdf]


  J. Lee, A. Liwo, D.R. Ripoll, J.Pillardy, J.A. Saunders, K.D. Gibson, and H.A. Scheraga.. (2000). “Hierarchical energy-based approach to protein-structure prediction; blind-test evaluation with CASP3 targets”. Int. J. Quant. Chem. 77, 90-117. [pdf] 


``A Molecular Switch for Biological Logic Gates: Conformational Studies.'' G. Ashkenazi, D. R. Ripoll, N. Lotan, H. A. Scheraga. (1997). Biosensors & Bioelectronics 12, 85-95. [pdf]




J.A. Vila, D.R. Ripoll and H.A. Scheraga. (2001). “Influence of Lysine Content and pH on the Stability of Alanine-Based Co-polypeptides”. Biopolymers, 58, 235-246. [pdf]

 J.A. Vila, D.R. Ripoll and  H. A. Scheraga. (2000). “Physical reasons for the unusual α-helix stabilization afforded by charged or neutral polar residues in alanine-rich peptides”. Proc. Natl. Acad. Sci. USA. 97, 13075-13079. [pdf]

Coupling between Folding and Ionization Equilibrium. Effects of pH on the Conformational Preference of Oligopeptides. D. Ripoll, Y. Vorabjev, A. Liwo, H. Scheraga and J. Vila. (1996). J. Mol. Biol. 264, 770-783. [pdf]

To see another figure showing the electrostatic field and surface potential generated by one of the lowest energy conformation click here.


M. Nanias, M. Chinchio, J. Pillardy, D.R. Ripoll, and H. A. Scheraga. (2003). “Packing helices in proteins by global optimization of a potential energy function. Proc. Natl. Acad. Sci. USA, 100, 1706-1710. [pdf]





``Implementation of ECEPP-based programs on the IBM SP2 and the SGI Power Challenge Computers''. T. O'Donnell, S. Hotovy, M. Pottle, D. Ripoll and H. Scheraga. (1996). Lecture Notes in Computer Science; vol. 1067: High-Performance Computing and Networking. Liddell,H., Colbrook, A., Hertzberger, B. and Sloot, P. Eds. Springer-Verlag, Berlin; Heildelberg; New York. 365-372.
``Implementation of the ECEPP Algorithm, the Monte Carlo Minimization Method, and the Electrostatically Driven Monte Carlo Method on the Kendal Square Research KSR1 Computer. D.R. Ripoll, M. S. Pottle, K. Gibson, A. Liwo and H. A. Scheraga. (1995) J. Comp. Chem. 16, 1153-1163.