IBBR Publications
Found 53 results
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Current status of protein force fields for molecular dynamics simulations. Methods Mol Biol. 2015 ;1215:47-71.
. Implementation of extended Lagrangian dynamics in GROMACS for polarizable simulations using the classical Drude oscillator model. J Comput Chem. 2015 ;36(19):1473-9.
. Molecular dynamics simulations of glycoproteins using CHARMM. Methods Mol Biol. 2015 ;1273:407-29.
. All-atom polarizable force field for DNA based on the classical Drude oscillator model. J Comput Chem. 2014 ;35(16):1219-39.
. CHARMM-GUI PDB manipulator for advanced modeling and simulations of proteins containing nonstandard residues. Adv Protein Chem Struct Biol. 2014 ;96:235-65.
ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers. Bioinformatics. 2014 ;30(12):1771-3.
. Balancing target flexibility and target denaturation in computational fragment-based inhibitor discovery. J Comput Chem. 2012 ;33(23):1880-91.
. NeXML: rich, extensible, and verifiable representation of comparative data and metadata. Syst Biol. 2012 ;61(4):675-89.
Development of CHARMM polarizable force field for nucleic acid bases based on the classical Drude oscillator model. J Phys Chem B. 2011 ;115(3):580-96.
. Evaluation of disorder predictions in CASP9. Proteins. 2011 ;79 Suppl 10:107-18.
. Impact of 2'-hydroxyl sampling on the conformational properties of RNA: update of the CHARMM all-atom additive force field for RNA. J Comput Chem. 2011 ;32(9):1929-43.
. Molecular simulations of dodecyl-β-maltoside micelles in water: influence of the headgroup conformation and force field parameters. J Phys Chem B. 2011 ;115(3):487-99.
. CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields. J Comput Chem. 2010 ;31(4):671-90.
Performance of ZDOCK and ZRANK in CAPRI rounds 13-19. Proteins. 2010 ;78(15):3104-10.
. CHARMM: the biomolecular simulation program. J Comput Chem. 2009 ;30(10):1545-614.
Outcome of a workshop on applications of protein models in biomedical research. Structure. 2009 ;17(2):151-9.
TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts. J Biomol NMR. 2009 ;44(4):213-23.
. Comparison of protein force fields for molecular dynamics simulations. Methods Mol Biol. 2008 ;443:63-88.
. Consistent blind protein structure generation from NMR chemical shift data. Proc Natl Acad Sci U S A. 2008 ;105(12):4685-90.
Protein-protein docking: overview and performance analysis. Methods Mol Biol. 2008 ;413:283-314.
. Proteopedia - a scientific 'wiki' bridging the rift between three-dimensional structure and function of biomacromolecules. Genome Biol. 2008 ;9(8):R121.
. Solution structure of tRNAVal from refinement of homology model against residual dipolar coupling and SAXS data. J Biomol NMR. 2008 ;42(2):99-109.
. Bio::NEXUS: a Perl API for the NEXUS format for comparative biological data. BMC Bioinformatics. 2007 ;8:191.
. The performance of ZDOCK and ZRANK in rounds 6-11 of CAPRI. Proteins. 2007 ;69(4):719-25.
. Mutation-biased adaptation in a protein NK model. Mol Biol Evol. 2006 ;23(10):1852-62.
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