BioShell-Threading: versatile Monte Carlo package for protein 3D threading.BMC Bioinformatics 15, 22, 2014.
Coarse-Grained Protein Models in Structure PredictionComputational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes, Springer Series in Bio-/Neuroinformatics, Adam Liwo, Ed. 1, 25-53, 2014.
BioShell Threader: protein homology detection based on sequence profiles and secondary structure profilesNucleic Acids Research 40, W257–62, 2012.
From coarse-grained to atomic-level characterization of protein dynamics: transition state for the folding of B domain of protein AThe Journal of Physical Chemistry B 116, 7026–32, 2012.
Modeling Protein Structures and their Complexes with Sparse Experimental DataFrom Computational Biophysics to Systems Biology (CBSB11) Proceedings 8, 49–52, 2012.
Multiscale Approach to Thermodynamics and Dynamics of a beta-Hairpin FoldingFrom Computational Biophysics to Systems Biology (CBSB11) Proceedings 8, 213–216, 2012.
Optimization of profile-to-profile alignment parameters for one-dimensional threadingJournal of Computational Biology 19, 879–86, 2012.
Optimization of protein modelsWiley Interdisciplinary Reviews: Computational Molecular Science 2, 479–493, 2012.
Fast and accurate methods for predicting short-range constraints in protein modelsJournal of Computer-Aided Molecular Design 22, 783–8, 2008.
Template-free predictions of three-dimensional protein structures: From first principles to knowledge-based potentialsPrediction of Protein Structures, Functions, and Interactions 117-142, 2008.
Backbone building from quadrilaterals: a fast and accurate algorithm for protein backbone reconstruction from alpha carbon coordinatesJournal of Computational Chemistry 28, 1593–7, 2007.
Comparative modeling without implicit sequence alignmentsBioinformatics (Oxford, England) 23, 2522–7, 2007.
Efficient scheme for optimization of parallel tempering Monte Carlo methodJournal of Physics: Condensed Matter 19, , 2007.
Towards the high-resolution protein structure prediction. Fast refinement of reduced models with all-atom force fieldBMC Structural Biology 7, 43, 2007.
T-Pile–a package for thermodynamic calculations for biomoleculesBioinformatics (Oxford, England) 23, 1840–1842, 2007.
BioShell–a package of tools for structural biology computationsBioinformatics (Oxford, England) 22, 621–622, 2006.