Publications
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Computational study of binding of epothilone A to β-tubulinActa Biochimica Polonica 58, 255–60, 2011.
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.
TOUCHSTONE: an ab initio protein structure prediction method that uses threading-based tertiary restraintsProceedings of the National Academy of Sciences of the United States of America 98, 10125–30, 2001.
Ab initio protein structure prediction on a genomic scale: application to the Mycoplasma genitalium genomeProceedings of the National Academy of Sciences of the United States of America 99, 5993–5998, 2002.
Theoretical models and simulations of polymer chainsPhysical Properties of Polymers Handbook , 2006.
Distance matrix-based approach to protein structure predictionJournal of Structural and Functional Genomics 10, 67–81, 2009.
Towards the high-resolution protein structure prediction. Fast refinement of reduced models with all-atom force fieldBMC Structural Biology 7, 43, 2007.
Modeling of Protein Structural Flexibility and Large-Scale Dynamics: Coarse-Grained Simulations and Elastic Network ModelsInternational Journal of Molecular Sciences 19, , 2018.
Multiscale approach to protein folding dynamicsMultiscale Approaches to Protein Modeling 281-294, 2011.
Characterization of protein-folding pathways by reduced-space modelingProceedings of the National Academy of Sciences of the United States of America 104, 12330–5, 2007.
Designing an Automatic Pipeline for Protein Structure Prediction Designing an Automatic Pipeline for Protein Structure PredictionFrom Computational Biophysics to Systems Biology (CBSB08) 40, 105–108, 2008.
Coarse-Grained Modeling of Protein DynamicsComputational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes, Springer Series in Bio-/Neuroinformatics, Adam Liwo, Ed. 1, 55-79, 2014.
Simulation of chaperonin effect on protein folding: a shift from nucleation-condensation to framework mechanismJournal of the American Chemical Society 133, 10283–9, 2011.
Structure prediction of the second extracellular loop in G-protein-coupled receptorsBiophysical Journal 106, 2408–2416, 2014.
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.
Denatured proteins and early folding intermediates simulated in a reduced conformational spaceActa Biochimica Polonica 53, 131–143, 2006.
Folding pathway of the b1 domain of protein G explored by multiscale modelingBiophysical Journal 94, 726–36, 2008.
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.
Protein Dynamics Simulations Using Coarse-Grained ModelsComputational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes: From Bioinformatics to Molecular Quantum Mechanics 61–87, 2019.
One-Dimensional Structural Properties of Proteins in the Coarse-Grained CABS ModelMethods in Molecular Biology 1484, 83-113, 2017.
Uncharacterized DUF1574 leptospira proteins are SGNH hydrolasesCell Cycle (Georgetown, Tex.) 7, 542–4, 2008.
Monte Carlo study of dynamics of the multichain polymer system on the tetrahedral latticeThe Journal of Chemical Physics 79, 1523-1526, 1983.
Application of a high coordination lattice model in protein structure predictionProceedings of HRLC Workshop pp, 100–130, 1998.