Absolute free energies estimated by combining precalculated molecular fragment libraries. - Xin Zhang 011; Artem B. Mamonov; Daniel M. Zuckerman (J. Comput. Chem., 2009)

Extending fragment-based free energy calculations with library monte carlo simulation: Annealing in interaction space. - Steven Lettieri; Artem B. Mamonov; Daniel M. Zuckerman (J. Comput. Chem., 2011)

Rapid sampling of all-atom peptides using a library-based polymer-growth approach. - Artem B. Mamonov; Xin Zhang 011; Daniel M. Zuckerman (J. Comput. Chem., 2011)

A message passing approach to Side Chain Positioning with applications in protein docking refinement. - Mohammad Moghadasi; Dima Kozakov; Artem B. Mamonov; Pirooz Vakili; Sandor Vajda; Ioannis Ch. Paschalidis (CDC, 2012)

Accounting for observed small angle X-ray scattering profile in the protein-protein docking server cluspro. - Bing Xia; Artem B. Mamonov; Seppe Leysen; Karen N. Allen; Sergei V. Strelkov; Ioannis Ch. Paschalidis; Sandor Vajda; Dima Kozakov (J. Comput. Chem., 2015)

The Impact of Side-Chain Packing on Protein Docking Refinement. - Mohammad Moghadasi; Hanieh Mirzaei; Artem B. Mamonov; Pirooz Vakili; Sandor Vajda; Ioannis Ch. Paschalidis; Dima Kozakov (J. Chem. Inf. Model., 2015)

Focused grid-based resampling for protein docking and mapping. - Artem B. Mamonov; Mohammad Moghadasi; Hanieh Mirzaei; Shahrooz Zarbafian; Laurie E. Grove; Tanggis Bohnuud; Pirooz Vakili; Ioannis Ch. Paschalidis; Sandor Vajda; Dima Kozakov (J. Comput. Chem., 2016)

Protein-ligand docking using FFT based sampling: D3R case study. - Dzmitry Padhorny; David R. Hall; Hanieh Mirzaei; Artem B. Mamonov; Mohammad Moghadasi; Andrey Alekseenko; Dmitri Beglov; Dima Kozakov (J. Comput. Aided Mol. Des., 2018)