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On the Importance of Hydrodynamic Interactions in Lipid Membrane Formation. Biophysical Journal. 104(1):96-105. PDF. 2013.
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Dynamic simulation of concentrated macromolecular solutions with screened long-range hydrodynamic interactions: Algorithm and limitations. Journal of Chemical Physics. 139:121922-1. PDF. 2013.
Multiple Time Step Brownian Dynamics for Long Time Simulation of Biomolecules. Molecular Simulation. 29(8):471-478.. 2003.
Krylov subspace methods for computing hydrodynamic interactions in Brownian dynamics simulations. The Journal of Chemical Physics. 137:064106. PDF. 2012.
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Development of an Atomistic Brownian Dynamics Algorithm with Implicit Solvent Model for Long Time Simulation.. Journal of Computer Chemistry, Japan. 1(3):115-122.. 2002.
Importance of excluded volume and hydrodynamic interactions on macromolecular diffusion in vivo. International Conference of the Quantum Bio-Informatics IV. 30:378-387. PDF. 2013.
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Identification of metabolites with anticancer properties by computational metabolomics. Molecular cancer. 7:57. PDF. 2008.
EFICAz2: enzyme function inference by a combined approach enhanced by machine learning. BMC bioinformatics. 10:107. PDF. 2009.
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Large-scale assessment of the utility of low-resolution protein structures for biochemical function assignment. Bioinformatics (Oxford, England). 20(7):1087-96. PDF Supplementary Data. 2004.
High precision multi-genome scale reannotation of enzyme function by EFICAz. BMC genomics. 7:315. PDF. 2006.
Development of a structure based protein function prediction method: Calcium binding protein. Chem-Bio Informatics Journal. 3:96-113.. 2003.
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Quantifying the structural requirements of the folding transition state of protein A and other systems. Journal of molecular biology. 381(5):1362-81.. 2008.
Psi-constrained simulations of protein folding transition states: implications for calculating phi. Journal of molecular biology. 386(4):920-8.. 2009.
Finding the needle in a haystack: educing native folds from ambiguousab initio protein structure predictions. Journal of Computational Chemistry. 22(3):339-353. PDF. 2001.
Local propensities and statistical potentials of backbone dihedral angles in proteins. Journal of molecular biology. 342(2):635-49. PDF. 2004.
Universal similarity measure for comparing protein structures. Biopolymers. 59(5):305-9. PDF. 2001.
A scoring function for docking ligands to low-resolution protein structures. Journal of computational chemistry. 26(4):374-83. PDF. 2005.
Protein fragment reconstruction using various modeling techniques. Journal of computer-aided molecular design. 17(11):725-38. PDF. 2003.
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Early-stage folding in proteins (in silico) sequence-to-structure relation. Journal of biomedicine & biotechnology. 2005(2):65-79. PDF. 2005.
Q-Dock(LHM): Low-resolution refinement for ligand comparative modeling. Journal of computational chemistry. 31(5):1093-105. PDF. 2010.
Q-Dock: Low-resolution flexible ligand docking with pocket-specific threading restraints. Journal of computational chemistry. 29(10):1574-88. PDF Supplementary Data. 2008.
Hydrophobic collapse in (in silico) protein folding. Computational biology and chemistry. 30(4):255-67. PDF. 2006.
Prediction of functional sites based on the fuzzy oil drop model. PLoS computational biology. 3(5):e94. PDF. 2007.
What is the relationship between the global structures of apo and holo proteins? Proteins. 70(2):363-77. PDF Supplementary Data. 2008.
Limited conformational space for early-stage protein folding simulation.. Bioinformatics (Oxford, England). 20(2):199-205. PDF. 2004.
Conservative secondary structure motifs already present in early-stage folding (in silico) as found in serpines family. Journal of theoretical biology. 251(2):275-85. PDF. 2008.
SPI--structure predictability index for protein sequences.. In silico biology. 5(3):227-37. PDF. 2005.
Hydrophobic collapse in late-stage folding (in silico) of bovine pancreatic trypsin inhibitor. Biochimie. 88(9):1229-39. PDF. 2006.
The utility of geometrical and chemical restraint information extracted from predicted ligand-binding sites in protein structure refinement. Journal of Structural Biology. 173(3):558-569. PDF. 2011.
A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation. Proceedings of the National Academy of Sciences of the United States of America. 105(1):129-34. PDF Supplementary Data. 2008.
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