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pyDockWEB: a web server for rigid-body protein-protein docking using electrostatics and desolvation scoring. Bioinformatics (Oxford, England) 29, 1698-9 (2013).
pyDockCG: new coarse-grained potential for protein-protein docking. The journal of physical chemistry. B 115, 6032-9 (2011).
A protein-RNA docking benchmark (II): extended set from experimental and homology modeling data. Proteins 80, 1872-82 (2012).
Prediction of protein-binding areas by small-world residue networks and application to docking. BMC bioinformatics 12, 378 (2011).
nucleR: a package for non-parametric nucleosome positioning. Bioinformatics (Oxford, England) 27, 2149-50 (2011).
Modulating O2 reactivity in a fungal flavoenzyme: involvement of aryl-alcohol oxidase Phe-501 contiguous to catalytic histidine. The Journal of biological chemistry 286, 41105-14 (2011).
Importance of accurate charges in molecular docking: quantum mechanical/molecular mechanical (QM/MM) approach. Journal of computational chemistry 26, 915-31 (2005).
Exploration of conformational transition pathways from coarse-grained simulations. Bioinformatics (Oxford, England) 29, 1980-6 (2013).
Evidence for transcript networks composed of chimeric RNAs in human cells. PloS one 7, e28213 (2012).
Computational modeling of the catalytic reaction in triosephosphate isomerase. Journal of molecular biology 337, 227-39 (2004).
A binding mechanism in protein-nucleotide interactions: implication for U1A RNA binding. Proceedings of the National Academy of Sciences of the United States of America 102, 3954-9 (2005).