Export 37 results:Author Title Type [ Year]
Filters: Keyword is Models, Molecular [Clear All Filters]
Conformational transitions in human translin enable nucleic acid binding. Nucleic acids research 41, 9956-66 (2013).
Allosteric conversation in the androgen receptor ligand-binding domain surfaces. Molecular endocrinology (Baltimore, Md.) 26, 1078-90 (2012).
Defining the nature of thermal intermediate in 3 state folding proteins: apoflavodoxin, a study case. PLoS computational biology 8, e1002647 (2012).
H-bond network optimization in protein-protein complexes: are all-atom force field scores enough?. Proteins 80, 818-24 (2012).
A protein-RNA docking benchmark (II): extended set from experimental and homology modeling data. Proteins 80, 1872-82 (2012).
Community-wide assessment of protein-interface modeling suggests improvements to design methodology. Journal of molecular biology 414, 289-302 (2011).
Electron transfer pathways in cytochrome c oxidase. Biochimica et biophysica acta 1807, 1305-13 (2011).
LRR conservation mapping to predict functional sites within protein leucine-rich repeat domains. PloS one 6, e21614 (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).
Molecular basis of substrate-induced permeation by an amino acid antiporter. Proceedings of the National Academy of Sciences of the United States of America 108, 3935-40 (2011).
The native ensemble and folding of a protein molten-globule: functional consequence of downhill folding. Journal of the American Chemical Society 133, 12154-61 (2011).
Prediction of protein-binding areas by small-world residue networks and application to docking. BMC bioinformatics 12, 378 (2011).
The protein folding transition-state ensemble from a Gō-like model. Physical chemistry chemical physics : PCCP 13, 15166-74 (2011).
Scoring by intermolecular pairwise propensities of exposed residues (SIPPER): a new efficient potential for protein-protein docking. Journal of chemical information and modeling 51, 370-7 (2011).
Structural analysis of an equilibrium folding intermediate in the apoflavodoxin native ensemble by small-angle X-ray scattering. Journal of molecular biology 406, 604-19 (2011).
MoDEL (Molecular Dynamics Extended Library): a database of atomistic molecular dynamics trajectories. Structure (London, England : 1993) 18, 1399-409 (2010).
Ligand migration in the truncated hemoglobin-II from Mycobacterium tuberculosis: the role of G8 tryptophan. The Journal of biological chemistry 284, 3106-16 (2009).
Raman study of mechanically induced oxygenation state transition of red blood cells using optical tweezers. Biophysical journal 96, 209-16 (2009).
Role of Pre-A motif in nitric oxide scavenging by truncated hemoglobin, HbN, of Mycobacterium tuberculosis. The Journal of biological chemistry 284, 14457-68 (2009).
Electron transfer in the P450cam/PDX complex. The QM/MM e-pathway. The journal of physical chemistry. A 112, 12989-94 (2008).
Heme electron transfer in peroxidases: the propionate e-pathway. The journal of physical chemistry. B 112, 13460-4 (2008).
Mapping protein electron transfer pathways with QM/MM methods. Journal of the Royal Society, Interface / the Royal Society 5 Suppl 3, S233-9 (2008).
Mechanism of product release in NO detoxification from Mycobacterium tuberculosis truncated hemoglobin N. Journal of the American Chemical Society 130, 1688-93 (2008).
Mechanism of thermal decomposition of carbamoyl phosphate and its stabilization by aspartate and ornithine transcarbamoylases. Proceedings of the National Academy of Sciences of the United States of America 105, 16918-23 (2008).
Nitric oxide reactivity with globins as investigated through computer simulation. Methods in enzymology 437, 477-98 (2008).
Functional and structural characterization of the first prokaryotic member of the L-amino acid transporter (LAT) family: a model for APC transporters. The Journal of biological chemistry 282, 13270-81 (2007).
A quantum-chemical picture of hemoglobin affinity. Proceedings of the National Academy of Sciences of the United States of America 104, 18451-5 (2007).
Hydrogen bonding pathways in human dihydroorotate dehydrogenase. The journal of physical chemistry. B 110, 19704-10 (2006).
Modeling of ligation-induced helix/loop displacements in myoglobin: toward an understanding of hemoglobin allostery. Journal of the American Chemical Society 128, 5427-35 (2006).
The role of the heme propionates in heme biochemistry. Journal of inorganic biochemistry 100, 755-60 (2006).
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).
Importance of accurate charges in molecular docking: quantum mechanical/molecular mechanical (QM/MM) approach. Journal of computational chemistry 26, 915-31 (2005).
Computational modeling of the catalytic reaction in triosephosphate isomerase. Journal of molecular biology 337, 227-39 (2004).
Cytochrome P450CAM enzymatic catalysis cycle: a quantum mechanics/molecular mechanics study. Journal of the American Chemical Society 126, 8501-8 (2004).
Peripheral heme substituents control the hydrogen-atom abstraction chemistry in cytochromes P450. Proceedings of the National Academy of Sciences of the United States of America 100, 6998-7002 (2003).
Dynamics of alkane hydroxylation at the non-heme diiron center in methane monooxygenase. Journal of the American Chemical Society 124, 3377-84 (2002).
Proton-transfer dynamics in the activation of cytochrome P450eryF. Journal of the American Chemical Society 124, 1430-7 (2002).