A parallel Monte Carlo search algorithm for the conformational analysis of proteins. - Daniel R. Ripoll; Stephen J. Thomas (SC, 1990)

A parallel Monte Carlo search algorithm for the conformational analysis of polypeptides. - Daniel R. Ripoll; Stephen J. Thomas (J. Supercomput., 1992)

Implementation of the ECEPP Algorithm, the Monte Carlo Minimization Method, and the Electrostatically Driven Monte Carlo Method on the Kendall Square Research KSR1 Computer. - Daniel R. Ripoll; Marcia S. Pottle; Kenneth D. Gibson; Harold A. Scheraga; Adam Liwo (J. Comput. Chem., 1995)

Implementation of ECEPP-Based Programs on the IBM SP2 and the SGI Power Challenge Computers. - Timothy J. O'Donnell; Steven Hotovy; Marcia S. Pottle; Daniel R. Ripoll; Harold A. Scheraga (HPCN Europe, 1996)

Surmounting the Multiple-Minima Problem in Protein Folding. - Harold A. Scheraga; Jooyoung Lee 002; Jaroslaw Pillardy; Yuan-Jie Ye; Adam Liwo; Daniel R. Ripoll (J. Glob. Optim., 1999)

UNRES: a united-residue force field for energy-based prediction of protein structure - orgin and significance of multibody terms. - Adam Liwo; Jaroslaw Pillardy; Cezary Czaplewski; Jooyoung Lee 002; Daniel R. Ripoll; Malgorzata Groth; Sylwia Rodziewicz-Motowidlo; Rajmund Kazmierkiewicz; Ryszard J. Wawak; Stanislaw Oldziej; Harold A. Scheraga (RECOMB, 2000)

Evolution of physics-based methodology for exploring the conformational energy landscape of proteins. - Harold A. Scheraga; Jaroslaw Pillardy; Adam Liwo; Jooyoung Lee 002; Cezary Czaplewski; Daniel R. Ripoll; William J. Wedemeyer; Yelena A. Arnautova (J. Comput. Chem., 2002)

Global Optimization in Protein Folding. - Daniel R. Ripoll; Adam Liwo; Harold A. Scheraga (Encyclopedia of Optimization, 2009)

Quantitative Predictions of Binding Free Energy Changes in Drug-Resistant Influenza Neuraminidase. - Daniel R. Ripoll; Ilja V. Khavrutskii; Sidhartha Chaudhury; Jin Liu 005; Robert A. Kuschner; Anders Wallqvist; Jaques Reifman (PLoS Comput. Biol., 2012)

Using the antibody-antigen binding interface to train image-based deep neural networks for antibody-epitope classification. - Daniel R. Ripoll; Sidhartha Chaudhury; Anders Wallqvist (PLoS Comput. Biol., 2021)