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.
Theoretical study of molecular mechanism of binding TRAP220 coactivator to Retinoid X Receptor alpha, activated by 9-cis retinoic acidThe Journal of Steroid Biochemistry and Molecular Biology 121, 124–9, 2010.
Contact prediction in protein modeling: scoring, folding and refinement of coarse-grained modelsBMC Structural Biology 8, 36, 2008.
Fast and accurate methods for predicting short-range constraints in protein modelsJournal of Computer-Aided Molecular Design 22, 783–8, 2008.
Folding pathway of the b1 domain of protein G explored by multiscale modelingBiophysical Journal 94, 726–36, 2008.
Predicting the complex structure and functional motions of the outer membrane transporter and signal transducer FecABiophysical journal 94, 2482–91, 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.
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.
Comparative modeling without implicit sequence alignmentsBioinformatics (Oxford, England) 23, 2522–7, 2007.
Protein structure prediction: combining de novo modeling with sparse experimental dataJournal of Computational Chemistry 28, 1668–76, 2007.
Steps towards flexible docking: modeling of three-dimensional structures of the nuclear receptors bound with peptide ligands mimicking co-activators' sequencesThe Journal of Steroid Biochemistry and Molecular Biology 103, 357–60, 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.