Published in J Mol Biol on January 04, 2010
Mitochondrial processing peptidase regulates PINK1 processing, import and Parkin recruitment. EMBO Rep (2012) 2.08
A computational study of the glycine-rich loop of mitochondrial processing peptidase. PLoS One (2013) 0.82
Proteomic responses of drought-tolerant and drought-sensitive cotton varieties to drought stress. Mol Genet Genomics (2016) 0.78
An Advanced System of the Mitochondrial Processing Peptidase and Core Protein Family in Trypanosoma brucei and Multiple Origins of the Core I Subunit in Eukaryotes. Genome Biol Evol (2013) 0.77
CAVER: a new tool to explore routes from protein clefts, pockets and cavities. BMC Bioinformatics (2006) 4.11
Functionalization of graphene: covalent and non-covalent approaches, derivatives and applications. Chem Rev (2012) 3.19
The molecular basis of vascular lumen formation in the developing mouse aorta. Dev Cell (2009) 3.08
EphA-Ephrin-A-mediated beta cell communication regulates insulin secretion from pancreatic islets. Cell (2007) 2.81
MOLE: a Voronoi diagram-based explorer of molecular channels, pores, and tunnels. Structure (2007) 2.49
Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles. J Chem Theory Comput (2011) 2.12
Molecular dynamics and quantum mechanics of RNA: conformational and chemical change we can believe in. Acc Chem Res (2010) 1.40
Fluorescence lifetime-resolved pH imaging of living cells. Cytometry A (2003) 1.40
Redesigning dehalogenase access tunnels as a strategy for degrading an anthropogenic substrate. Nat Chem Biol (2009) 1.39
MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels. Nucleic Acids Res (2012) 1.34
Identification of tunnels in proteins, nucleic acids, inorganic materials and molecular ensembles. Biotechnol J (2007) 1.31
MOLE 2.0: advanced approach for analysis of biomacromolecular channels. J Cheminform (2013) 1.26
Solution structure of the ESCRT-I complex by small-angle X-ray scattering, EPR, and FRET spectroscopy. Proc Natl Acad Sci U S A (2011) 1.22
Membrane position of ibuprofen agrees with suggested access path entrance to cytochrome P450 2C9 active site. J Phys Chem A (2011) 1.21
Crystal structure of haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26 at 0.95 A resolution: dynamics of catalytic residues. Biochemistry (2004) 1.19
14-3-3 Protein interacts with nuclear localization sequence of forkhead transcription factor FoxO4. Biochemistry (2005) 1.18
Flexibility of human cytochromes P450: molecular dynamics reveals differences between CYPs 3A4, 2C9, and 2A6, which correlate with their substrate preferences. J Phys Chem B (2008) 1.16
Cleavage site selection within a folded substrate by the ATP-dependent lon protease. J Biol Chem (2005) 1.16
Environmental applications of chemically pure natural ferrihydrite. Environ Sci Technol (2007) 1.15
Foxj1 regulates floor plate cilia architecture and modifies the response of cells to sonic hedgehog signalling. Development (2010) 1.13
Fluorescent zinc indicators for neurobiology. J Neurosci Methods (2002) 1.12
In vivo kinetics of U4/U6·U5 tri-snRNP formation in Cajal bodies. Mol Biol Cell (2010) 1.11
Protonation states of the key active site residues and structural dynamics of the glmS riboswitch as revealed by molecular dynamics. J Phys Chem B (2010) 1.11
Reference simulations of noncanonical nucleic acids with different χ variants of the AMBER force field: quadruplex DNA, quadruplex RNA and Z-DNA. J Chem Theory Comput (2012) 1.09
Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters. J Chem Theory Comput (2013) 1.09
The 14-3-3 protein affects the conformation of the regulatory domain of human tyrosine hydroxylase. Biochemistry (2008) 1.07
Extensive molecular dynamics simulations showing that canonical G8 and protonated A38H+ forms are most consistent with crystal structures of hairpin ribozyme. J Phys Chem B (2010) 1.07
Adsorption of small organic molecules on graphene. J Am Chem Soc (2013) 1.04
Activation and inhibition of cyclin-dependent kinase-2 by phosphorylation; a molecular dynamics study reveals the functional importance of the glycine-rich loop. Protein Sci (2004) 1.04
Reductive evolution of the mitochondrial processing peptidases of the unicellular parasites trichomonas vaginalis and giardia intestinalis. PLoS Pathog (2008) 1.02
Dynamics and hydration of the active sites of mammalian cytochromes P450 probed by molecular dynamics simulations. Curr Drug Metab (2012) 1.02
l-3,4-Dihydroxyphenyl alanine-extradiol cleavage is followed by intramolecular cyclization in lincomycin biosynthesis. Eur J Biochem (2004) 1.01
Dependence of A-RNA simulations on the choice of the force field and salt strength. Phys Chem Chem Phys (2009) 1.01
Force-field dependence of chignolin folding and misfolding: comparison with experiment and redesign. Biophys J (2012) 0.97
General base catalysis for cleavage by the active-site cytosine of the hepatitis delta virus ribozyme: QM/MM calculations establish chemical feasibility. J Phys Chem B (2008) 0.96
Simulations of A-RNA duplexes. The effect of sequence, solute force field, water model, and salt concentration. J Phys Chem B (2012) 0.96
14-3-3 protein masks the DNA binding interface of forkhead transcription factor FOXO4. J Biol Chem (2009) 0.95
Theoretical studies of RNA catalysis: hybrid QM/MM methods and their comparison with MD and QM. Methods (2009) 0.95
14-3-3 protein C-terminal stretch occupies ligand binding groove and is displaced by phosphopeptide binding. J Biol Chem (2004) 0.95
The mechanism of inhibition of the cyclin-dependent kinase-2 as revealed by the molecular dynamics study on the complex CDK2 with the peptide substrate HHASPRK. Protein Sci (2005) 0.94
Mechanism of enhanced conversion of 1,2,3-trichloropropane by mutant haloalkane dehalogenase revealed by molecular modeling. J Comput Aided Mol Des (2006) 0.94
14-3-3zeta C-terminal stretch changes its conformation upon ligand binding and phosphorylation at Thr232. J Biol Chem (2003) 0.93
Genome-wide occupancy links Hoxa2 to Wnt-β-catenin signaling in mouse embryonic development. Nucleic Acids Res (2012) 0.92
How to understand quantum chemical computations on DNA and RNA systems? A practical guide for non-specialists. Methods (2013) 0.92
Formation of cardiovascular tubes in invertebrates and vertebrates. Cell Mol Life Sci (2010) 0.92
A biosensor for the detection of triazine and phenylurea herbicides designed using Photosystem II coupled to a screen-printed electrode. Biotechnol Bioeng (2002) 0.92
Covalent binding of cisplatin impairs the function of Na(+)/K(+)-ATPase by binding to its cytoplasmic part. Biochem Pharmacol (2012) 0.92
Large-scale compensation of errors in pairwise-additive empirical force fields: comparison of AMBER intermolecular terms with rigorous DFT-SAPT calculations. Phys Chem Chem Phys (2010) 0.90
Transferable scoring function based on semiempirical quantum mechanical PM6-DH2 method: CDK2 with 15 structurally diverse inhibitors. J Comput Aided Mol Des (2011) 0.90
Molecular mechanism of preQ1 riboswitch action: a molecular dynamics study. J Phys Chem B (2012) 0.90
Mutasynthesis of lincomycin derivatives with activity against drug-resistant staphylococci. Antimicrob Agents Chemother (2009) 0.90
Effect of guanine to inosine substitution on stability of canonical DNA and RNA duplexes: molecular dynamics thermodynamics integration study. J Phys Chem B (2013) 0.89
Both the N-terminal loop and wing W2 of the forkhead domain of transcription factor Foxo4 are important for DNA binding. J Biol Chem (2007) 0.89
Graphene fluoride: a stable stoichiometric graphene derivative and its chemical conversion to graphene. Small (2010) 0.89
Maximum entropy analysis of analytically simulated complex fluorescence decays. J Fluoresc (2010) 0.88
The DNA and RNA sugar-phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies. Phys Chem Chem Phys (2012) 0.87
Positioning of antioxidant quercetin and its metabolites in lipid bilayer membranes: implication for their lipid-peroxidation inhibition. J Phys Chem B (2012) 0.87
Functional flexibility of human cyclin-dependent kinase-2 and its evolutionary conservation. Protein Sci (2007) 0.87
The Nature of the Binding of Au, Ag, and Pd to Benzene, Coronene, and Graphene: From Benchmark CCSD(T) Calculations to Plane-Wave DFT Calculations. J Chem Theory Comput (2011) 0.86
Convergence of Free Energy Profile of Coumarin in Lipid Bilayer. J Chem Theory Comput (2012) 0.86
Interaction energies for the purine inhibitor roscovitine with cyclin-dependent kinase 2: correlated ab initio quantum-chemical, DFT and empirical calculations. Chemistry (2006) 0.86
QM/MM studies of hairpin ribozyme self-cleavage suggest the feasibility of multiple competing reaction mechanisms. J Phys Chem B (2011) 0.86
Behavior of human cytochromes P450 on lipid membranes. J Phys Chem B (2013) 0.86
Chemical nature of boron and nitrogen dopant atoms in graphene strongly influences its electronic properties. Phys Chem Chem Phys (2014) 0.86
Quantification of the interaction forces between metals and graphene by quantum chemical calculations and dynamic force measurements under ambient conditions. ACS Nano (2013) 0.86
Structural basis for the 14-3-3 protein-dependent inhibition of the regulator of G protein signaling 3 (RGS3) function. J Biol Chem (2011) 0.85
The C-terminal segment of yeast BMH proteins exhibits different structure compared to other 14-3-3 protein isoforms. Biochemistry (2010) 0.85
Noncanonical hydrogen bonding in nucleic acids. Benchmark evaluation of key base-phosphate interactions in folded RNA molecules using quantum-chemical calculations and molecular dynamics simulations. J Phys Chem A (2011) 0.84
Flexibility of human cytochrome P450 enzymes: molecular dynamics and spectroscopy reveal important function-related variations. Biochim Biophys Acta (2010) 0.84
14-3-3 protein interacts with and affects the structure of RGS domain of regulator of G protein signaling 3 (RGS3). J Struct Biol (2010) 0.84
Thiofluorographene-hydrophilic graphene derivative with semiconducting and genosensing properties. Adv Mater (2015) 0.83
HIV Rev self-assembly is linked to a molten-globule to compact structural transition. Biophys Chem (2004) 0.83
ATP and magnesium drive conformational changes of the Na+/K+-ATPase cytoplasmic headpiece. Biochim Biophys Acta (2009) 0.83
Substrate evokes translocation of both domains in the mitochondrial processing peptidase alpha-subunit during which the C-terminus acts as a stabilizing element. Biochem Biophys Res Commun (2004) 0.83
Lincomycin biosynthesis involves a tyrosine hydroxylating heme protein of an unusual enzyme family. PLoS One (2013) 0.83
Nature and magnitude of aromatic base stacking in DNA and RNA: Quantum chemistry, molecular mechanics, and experiment. Biopolymers (2013) 0.83
A cancer-derived mutation in the PSTAIRE helix of cyclin-dependent kinase 2 alters the stability of cyclin binding. Biochim Biophys Acta (2010) 0.82
Band gaps and structural properties of graphene halides and their derivates: a hybrid functional study with localized orbital basis sets. J Chem Phys (2012) 0.82
Density-functional, density-functional tight-binding, and wave function calculations on biomolecular systems. J Phys Chem A (2007) 0.82
The role of calcium in the conformational dynamics and thermal stability of the D-galactose/D-glucose-binding protein from Escherichia coli. Proteins (2005) 0.82
A computational study of the glycine-rich loop of mitochondrial processing peptidase. PLoS One (2013) 0.82
Halogenated graphenes: rapidly growing family of graphene derivatives. ACS Nano (2013) 0.82
Modelling of graphene functionalization. Phys Chem Chem Phys (2015) 0.82
Regulatory phosphorylation of cyclin-dependent kinase 2: insights from molecular dynamics simulations. J Mol Model (2008) 0.81
Fluorescence of sanguinarine: fundamental characteristics and analysis of interconversion between various forms. Anal Bioanal Chem (2009) 0.81
Fluorescence of sanguinarine: spectral changes on interaction with amino acids. Phys Chem Chem Phys (2010) 0.81