Combining Coarse-Grained Protein Models with Replica-Exchange All-Atom Molecular DynamicsInternational Journal of Molecular Sciences 14, 9893–9905, 2013.
Consistent View of Protein Fluctuations from All-Atom Molecular Dynamics and Coarse-Grained Dynamics with Knowledge-Based Force-FieldJournal of Chemical Theory and Computation 9, 119 - 125, 2013.
Distributions of amino acids suggest that certain residue types more effectively determine protein secondary structureJournal of Molecular Modeling 19, 4337-48, 2013.
Hysteresis as a Marker for Complex, Overlapping Landscapes in Proteins.Journal of Physicak Chemistry Letters 4, 180-188, 2013.
Assessment of the free binding energy of 1,25-dihydroxyvitamin D3 and its analogs with the human VDR receptor modelActa Biochimica Polonica 59, 653-660, 2012.
BioShell Threader: protein homology detection based on sequence profiles and secondary structure profilesNucleic Acids Research 40, W257–62, 2012.
Coarse-grained Protein Modeling: Dynamics, Folding Pathways and Mechanical UnfoldingFrom Computational Biophysics to Systems Biology (CBSB11) Proceedings 8, 83–90, 2012.
Conservation of complex knotting and slipknotting patterns in proteins.Proceedings of the National Academy of Sciences of the United States of America 109, E1715-23, 2012.
Elastic network normal modes provide a basis for protein structure refinementThe Journal of Chemical Physics 136, 195101, 2012.
Energy landscape of knotted protein folding.Proceedings of the National Academy of Sciences of the United States of America 109, 17783-8, 2012.
Fast learning optimized prediction methodology (FLOPRED) for protein secondary structure predictionJournal of Molecular Modeling 18, 4275–89, 2012.
Folding Simulations of the A and B Domains of Protein GThe Journal of Physical Chemistry B 116, 6645-6653, 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.
Genomics-aided structure prediction.Proceedings of the National Academy of Sciences of the United States of America 109, 10340-5, 2012.
How noise in force fields can affect the structural refinement of protein models?Proteins 80, 335–341, 2012.
Modeling Protein Structures and their Complexes with Sparse Experimental DataFrom Computational Biophysics to Systems Biology (CBSB11) Proceedings 8, 49–52, 2012.
Modelowanie Molekularne Białek Błonowych (Molecular Modeling of Membrane Proteins)Na pograniczu chemii i biologii (At the Treshold of Chemistry and Biology) vol. XXVIII, H. Koroniak, J. Barciszewski eds, Wydawnictwo Naukowe UAM, Poznań 223-238, 2012.