IBBR Publications

Found 53 results
Filters: Keyword is Software  [Clear All Filters]
2015
Lopes PEM, Guvench O, Mackerell AD. Current status of protein force fields for molecular dynamics simulations. Methods Mol Biol. 2015 ;1215:47-71.
Lemkul JA, Roux B, van der Spoel D, Mackerell AD. Implementation of extended Lagrangian dynamics in GROMACS for polarizable simulations using the classical Drude oscillator model. J Comput Chem. 2015 ;36(19):1473-9.
Mallajosyula SS, Jo S, Im W, Mackerell AD. Molecular dynamics simulations of glycoproteins using CHARMM. Methods Mol Biol. 2015 ;1273:407-29.
2014
Savelyev A, Mackerell AD. All-atom polarizable force field for DNA based on the classical Drude oscillator model. J Comput Chem. 2014 ;35(16):1219-39.
Jo S, Cheng X, Islam SM, Huang L, Rui H, Zhu A, Lee HSun, Qi Y, Han W, Vanommeslaeghe K, et al. CHARMM-GUI PDB manipulator for advanced modeling and simulations of proteins containing nonstandard residues. Adv Protein Chem Struct Biol. 2014 ;96:235-65.
Pierce BG, Wiehe K, Hwang H, Kim B-H, Vreven T, Weng Z. ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers. Bioinformatics. 2014 ;30(12):1771-3.
2012
Foster TJ, Mackerell AD, Guvench O. Balancing target flexibility and target denaturation in computational fragment-based inhibitor discovery. J Comput Chem. 2012 ;33(23):1880-91.
Vos RA, Balhoff JP, Caravas JA, Holder MT, Lapp H, Maddison WP, Midford PE, Priyam A, Sukumaran J, Xia X, et al. NeXML: rich, extensible, and verifiable representation of comparative data and metadata. Syst Biol. 2012 ;61(4):675-89.
2011
Baker CM, Anisimov VM, Mackerell AD. 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.
Monastyrskyy B, Fidelis K, Moult J, Tramontano A, Kryshtafovych A. Evaluation of disorder predictions in CASP9. Proteins. 2011 ;79 Suppl 10:107-18.
Denning EJ, U Priyakumar D, Nilsson L, Mackerell AD. 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.
Abel S, Dupradeau F-Y, E Raman P, Mackerell AD, Marchi M. 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.
2010
Vanommeslaeghe K, Hatcher E, Acharya C, Kundu S, Zhong S, Shim J, Darian E, Guvench O, Lopes P, Vorobyov I, et al. 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.
Hwang H, Vreven T, Pierce BG, Hung J-H, Weng Z. Performance of ZDOCK and ZRANK in CAPRI rounds 13-19. Proteins. 2010 ;78(15):3104-10.
2009
Brooks BR, Brooks CL, Mackerell AD, Nilsson L, Petrella RJ, Roux B, Won Y, Archontis G, Bartels C, Boresch S, et al. CHARMM: the biomolecular simulation program. J Comput Chem. 2009 ;30(10):1545-614.
Schwede T, Sali A, Honig B, Levitt M, Berman HM, Jones D, Brenner SE, Burley SK, Das R, Dokholyan NV, et al. Outcome of a workshop on applications of protein models in biomedical research. Structure. 2009 ;17(2):151-9.
Shen Y, Delaglio F, Cornilescu G, Bax A. TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts. J Biomol NMR. 2009 ;44(4):213-23.
2008
Guvench O, Mackerell AD. Comparison of protein force fields for molecular dynamics simulations. Methods Mol Biol. 2008 ;443:63-88.
Shen Y, Lange O, Delaglio F, Rossi P, Aramini JM, Liu G, Eletsky A, Wu Y, Singarapu KK, Lemak A, et al. Consistent blind protein structure generation from NMR chemical shift data. Proc Natl Acad Sci U S A. 2008 ;105(12):4685-90.
Wiehe K, Peterson MW, Pierce BG, Mintseris J, Weng Z. Protein-protein docking: overview and performance analysis. Methods Mol Biol. 2008 ;413:283-314.
Hodis E, Prilusky J, Martz E, Silman I, Moult J, Sussman JL. Proteopedia - a scientific 'wiki' bridging the rift between three-dimensional structure and function of biomacromolecules. Genome Biol. 2008 ;9(8):R121.
Grishaev A, Ying J, Canny MD, Pardi A, Bax A. Solution structure of tRNAVal from refinement of homology model against residual dipolar coupling and SAXS data. J Biomol NMR. 2008 ;42(2):99-109.
2007
Hladish T, Gopalan V, Liang C, Qiu W, Yang P, Stoltzfus A. Bio::NEXUS: a Perl API for the NEXUS format for comparative biological data. BMC Bioinformatics. 2007 ;8:191.
Wiehe K, Pierce BG, Tong WWei, Hwang H, Mintseris J, Weng Z. The performance of ZDOCK and ZRANK in rounds 6-11 of CAPRI. Proteins. 2007 ;69(4):719-25.
2006
Stoltzfus A. Mutation-biased adaptation in a protein NK model. Mol Biol Evol. 2006 ;23(10):1852-62.