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Importance of accurate charges in molecular docking: quantum mechanical/molecular mechanical (QM/MM) approach. Journal of computational chemistry 26, 915-31 (2005).
Evidence for transcript networks composed of chimeric RNAs in human cells. PloS one 7, e28213 (2012).
nucleR: a package for non-parametric nucleosome positioning. Bioinformatics (Oxford, England) 27, 2149-50 (2011).
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).
Computational modeling of the catalytic reaction in triosephosphate isomerase. Journal of molecular biology 337, 227-39 (2004).
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).
pyDockWEB: a web server for rigid-body protein-protein docking using electrostatics and desolvation scoring. Bioinformatics (Oxford, England) 29, 1698-9 (2013).
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).
Exploration of conformational transition pathways from coarse-grained simulations. Bioinformatics (Oxford, England) 29, 1980-6 (2013).
pyDockCG: new coarse-grained potential for protein-protein docking. The journal of physical chemistry. B 115, 6032-9 (2011).