New force replica exchange method and protein folding pathways probed by force-clamp techniqueThe Journal of Chemical Physics 128, 045103, 2008.
Predicting the complex structure and functional motions of the outer membrane transporter and signal transducer FecABiophysical journal 94, 2482–91, 2008.
Selection of optimal variants of Gō-like models of proteins through studies of stretching.Biophys J 95, 3174-91, 2008.
Stabilizing effect of knots on proteins.Proceedings of the National Academy of Sciences of the United States of America 105, 19714-9, 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.
Uncharacterized DUF1574 leptospira proteins are SGNH hydrolasesCell Cycle (Georgetown, Tex.) 7, 542–4, 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.
Computational analysis of the active sites in binary and ternary complexes of the vitamin D receptorThe Journal of Steroid Biochemistry and Molecular Biology 103, 305-9, 2007.
Efficient scheme for optimization of parallel tempering Monte Carlo methodJournal of Physics: Condensed Matter 19, , 2007.
Ideal amino acid exchange forms for approximating substitution matricesProteins: Structure, Function, Bioinformatics 69, 379–393, 2007.
Mechanical stretching of proteins—a theoretical survey of the Protein Data BankJournal of Physics: Condensed Matter 19, , 2007.
Protein structure prediction: combining de novo modeling with sparse experimental dataJournal of Computational Chemistry 28, 1668–76, 2007.
Refolding upon force quench and pathways of mechanical and thermal unfolding of ubiquitinBiophysical Journal 92, 547-61, 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.