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.
An Optimized Replica Exchange Molecular Dynamics ApproachFrom Computational Biophysics to Systems Biology (CBSB11) Proceedings 8, 91-94 , 2012.
Prediction of Experimental Phi Values in Protein Folding by Simulation with Knowledge-based Potentials: B Domain of Protein AFrom Computational Biophysics to Systems Biology (CBSB11) Proceedings 8, 79–82, 2012.
Protein Structure Prediction Using CABS – A Consensus ApproachFrom Computational Biophysics to Systems Biology (CBSB11) Proceedings 8, 29–32, 2012.
Structural features that predict real-value fluctuations of globular proteinsProteins 80, 1425–35, 2012.
13,13-Dimethyl-des-C,D analogues of (20S)-1α,25-dihydroxy-2-methylene-19-norvitamin D₃ (2MD): total synthesis, docking to the VDR, and biological evaluationBioorganic & Medicinal Chemistry 19, 7205-20, 2011.
Analysis and optimization of interactions between peptides mimicking the GD2 ganglioside and the monoclonal antibody 14G2aInternational Journal of Molecular Medicine 28, 47–57, 2011.
CABS-NMR–De novo tool for rapid global fold determination from chemical shifts, residual dipolar couplings and sparse methyl-methyl NOEsJournal of c\Computational Chemistry 32, 536–44, 2011.
Computational study of binding of epothilone A to β-tubulinActa Biochimica Polonica 58, 255–60, 2011.
Human telomerase model shows the role of the TEN domain in advancing the double helix for the next polymerization stepProceedings of the National Academy of Sciences of the United States of America 108, 9443–8, 2011.
Multiscale approach to protein folding dynamicsMultiscale Approaches to Protein Modeling 281-294, 2011.
Note: A simple picture of subdiffusive polymer motion from stochastic simulationsThe Journal of Chemical Physics 134, 056101, 2011.
Simulation of chaperonin effect on protein folding: a shift from nucleation-condensation to framework mechanismJournal of the American Chemical Society 133, 10283–9, 2011.
Universal geometrical factor of protein conformations as a consequence of energy minimizationEPL (Europhysics Letters) 96:68005 doi: 10.1209/0295-5075/96/68005, , 2011.
Coarse-grained Monte Carlo simulations of mucus: structure, dynamics, and thermodynamicsBiophysical Journal 99, 3507–16, 2010.
Mechanical unfolding of acylphosphatase studied by single-molecule force spectroscopy and MD simulationsBiophys J 99, 238-47, 2010.