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Combining Structural Aggregation Propensity and Stability Predictions To Redesign Protein SolubilityMolecular Pharmaceutics 15, 3846-3859, 2018.
Optimization of profile-to-profile alignment parameters for one-dimensional threadingJournal of Computational Biology 19, 879–86, 2012.
How noise in force fields can affect the structural refinement of protein models?Proteins 80, 335–341, 2012.
Coarse-grained Monte Carlo simulations of mucus: structure, dynamics, and thermodynamicsBiophysical Journal 99, 3507–16, 2010.
BioShell-Threading: versatile Monte Carlo package for protein 3D threading.BMC Bioinformatics 15, 22, 2014.
Note: A simple picture of subdiffusive polymer motion from stochastic simulationsThe Journal of Chemical Physics 134, 056101, 2011.
Elastic network normal modes provide a basis for protein structure refinementThe Journal of Chemical Physics 136, 195101, 2012.
Simulations of the Folding Pathway of TIM-type a/ß Barrel ProteinsProceedings of the National Academy of Sciences of the United States of America 89, 2629–2633, 1992.
Are proteins ideal mixtures of amino acids? Analysis of energy parameter setsProtein Science: a Publication of the Protein Society 4, 2107–2117, 1995.
A Topology Fingerprint Approach to the Inverse Protein Folding ProblemJournal of Molecular Biology 227, 227–238, 1992.
Lattice representations of globular proteins: How good are they?Journal of Computational Chemistry 14, 1194-1202 , 1993.
De novo and inverse folding predictions of protein structure and dynamicsJournal of Computer-Aided Molecular Design 7, 397–438, 1993.
Efficient scheme for optimization of parallel tempering Monte Carlo methodJournal of Physics: Condensed Matter 19, , 2007.
Exploring protein energy landscapes with hierarchical clusteringInternational Journal of Quantum Chemistry 105, 826–830, 2005.
BioShell–a package of tools for structural biology computationsBioinformatics (Oxford, England) 22, 621–622, 2006.
Protein structure prediction by tempering spatial constraintsJournal of Computer-Aided Molecular Design 19, 603–8, 2005.
Template-free predictions of three-dimensional protein structures: From first principles to knowledge-based potentialsPrediction of Protein Structures, Functions, and Interactions 117-142, 2008.
Optimization of protein modelsWiley Interdisciplinary Reviews: Computational Molecular Science 2, 479–493, 2012.
A new combination of replica exchange Monte Carlo and histogram analysis for protein folding and thermodynamicsThe Journal of Chemical Physics 115, 1569–1574, 2001.