A new approach to prediction of short-range conformational propensities in proteins. - Dominik Gront; Andrzej Kolinski (Bioinform., 2005)

HCPM - program for hierarchical clustering of protein models. - Dominik Gront; Andrzej Kolinski (Bioinform., 2005)

Protein structure prediction by tempering spatial constraints. - Dominik Gront; Andrzej Kolinski; Ulrich H. E. Hansmann (J. Comput. Aided Mol. Des., 2005)

BioShell - a package of tools for structural biology computations. - Dominik Gront; Andrzej Kolinski (Bioinform., 2006)

T-Pile - a package for thermodynamic calculations for biomolecules. - Dominik Gront; Andrzej Kolinski (Bioinform., 2007)

Comparative modeling without implicit sequence alignments. - Andrzej Kolinski; Dominik Gront (Bioinform., 2007)

Backbone building from quadrilaterals: A fast and accurate algorithm for protein backbone reconstruction from alpha carbon coordinates. - Dominik Gront; Sebastian Kmiecik; Andrzej Kolinski (J. Comput. Chem., 2007)

Utility library for structural bioinformatics. - Dominik Gront; Andrzej Kolinski (Bioinform., 2008)

Fast and accurate methods for predicting short-range constraints in protein models. - Dominik Gront; Andrzej Kolinski (J. Comput. Aided Mol. Des., 2008)

Optimization of Profile-to-Profile Alignment Parameters for One-Dimensional Threading. - Pawel Gniewek; Andrzej Kolinski; Dominik Gront (J. Comput. Biol., 2012)

BioShell Threader: protein homology detection based on sequence profiles and secondary structure profiles. - Dominik Gront; Maciej Blaszczyk; Piotr Wojciechowski 003; Andrzej Kolinski (Nucleic Acids Res., 2012)

BioShell-Threading: versatile Monte Carlo package for protein 3D threading. - Pawel Gniewek; Andrzej Kolinski; Andrzej Kloczkowski; Dominik Gront (BMC Bioinform., 2014)

Practical Considerations for Atomistic Structure Modeling with Cryo-EM Maps. - Doo Nam Kim; Dominik Gront; Karissa Y. Sanbonmatsu (J. Chem. Inf. Model., 2020)

Better together: Elements of successful scientific software development in a distributed collaborative community. - Julia Koehler Leman; Brian D. Weitzner; P. Douglas Renfrew; Steven M. Lewis; Rocco Moretti; Andrew M. Watkins; Vikram Khipple Mulligan; Sergey Lyskov; Jared Adolf-Bryfogle; Jason W. Labonte; Justyna Krys; RosettaCommons Consortium; et al. (PLoS Comput. Biol., 2020)

VisuaLife: library for interactive visualization in rich web applications. - Justyna Krys; Dominik Gront (Bioinform., 2021)