COPASI's Use In Macromolecular Biochemistry


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Jungmann R, Avendaño MS, Dai M, Woehrstein JB, Agasti SS, Feiger Z, Rodal A, Yin P (2016) Quantitative super-resolution imaging with qPAINT. Nature Methods 13:439–442 Laboratory Method Macromolecular Biochemistry Link
McClary WD (2016) Interactions of Cytochrome P450 3A4 with Phospholipid Bilayer Nanodiscs. PhD Thesis, Seattle, University of Washington. Biochemistry Macromolecular Biochemistry Link
Meng X, Firczuk H, Pietroni P, Westbrook R, Dacheux E, Mendes P, McCarthy JE (2016) Minimum-noise production of translation factor eIF4G maps to a mechanistically determined optimal rate control window for protein synthesis. Nucleic Acids Research 45:1015–1025 Biochemistry Macromolecular Biochemistry Link
Reichard EL, Chirico GG, Dewey WJ, Nassif ND, Bard KE, Millas NE, Kraut DA (2016) Substrate Ubiquitination Controls the Unfolding Ability of the Proteasome. Journal of Biological Chemistry 291:18547–18561 Biochemistry Macromolecular Biochemistry Link
Rentergent J, Driscoll MD, Hay S (2016) Time course analysis of enzyme-catalyzed DNA polymerization. Biochemistry 55:5622–5634 Biochemistry Enzymology Macromolecular Biochemistry Link

5 publications
Dacheux E, Firczuk H, McCarthy JEG (2015) Rate control in yeast protein synthesis at the population and single-cell levels. Bioch. Soc. Trans. 43:1266-70 Macromolecular Biochemistry Link
Daneshjou N, Sieracki N, van Nieuw Amerongen GP, Schwartz MA, Komarova YA, Malik AB, Conway DE (2015) Rac1 functions as a reversible tension modulator to stabilize VE-cadherin trans-interaction. J. Cell Biol. 208:23-32 Macromolecular Biochemistry Cell Biology Link
Dornseifer S, Willkomm S, Far RK, Liebschwager J, Beltsiou F, Frank K, Laufer SD, Martinetz T, Sczakiel G, Claussen JC, Restle T (2015) RNAi revised - target mRNA-dependent enhancement of gene silencing. Nucl. Acids Res. 43:10623-32. Macromolecular Biochemistry Genetics Link
Dutta-Roy R, Rosenmund C, Edelstein SJ, Le Novère N (2015) Ligand-Dependent Opening of the Multiple AMPA Receptor Conductance States: A Concerted Model. PLoS ONE 10:e0116616 Physiology Macromolecular Biochemistry Link
Hudson DA, Gannon SA, Thorpe C, (2015) Oxidative protein folding: From thiol-disulfide exchange reactions to the redox poise of the endoplasmic reticulum. Free Radicals Biol. Med. 80:171-182 Macromolecular Biochemistry Link
Karapetyan S, Buchler NE (2015) Role of DNA binding sites and slow unbinding kinetics in titration-based oscillators. Phys. Rev. E 92:062712 Macromolecular Biochemistry Theory Link
Lee TW, Yang AS-P, Brittain T, Birch NP (2015) An analysis approach to identify specific functional sites in orthologous proteins using sequence and structural information: Application to neuroserpin reveals regions that differentially regulate inhibitory activity. Proteins Struct. Funct. Bioinformatics 83:135-52 Macromolecular Biochemistry Link
Rastgou Talemi S, Kollarovic G, Lapytsko A, Schaber J (2015) Development of a robust DNA damage model including persistent telomere-associated damage with application to secondary cancer risk assessment. Sci. Rep. 5:13540 Genetics Macromolecular Biochemistry Link
Roy RD, Stefan MI (2015) Cooperative Binding Mitigates the High-Dose Hook Effect. BioArchive doi:10.1101/021717 Theory Macromolecular Biochemistry Link
Subburaj Y, Ros U, Hermann E, Tong R, García-Sáez AJ (2015) Toxicity of an alpha-Pore-forming Toxin Depends on the Assembly Mechanism on the Target Membrane as Revealed by Single Molecule Imaging. J. Biol. Chem. 290:4856-4865 Macromolecular Biochemistry Link
Zhou J, Aponte-Santamaría C, Sturm S, Bullerjahn JT, Bronowska A, Gräter F (2015) Mechanism of Focal Adhesion Kinase Mechanosensing. PLoS Comput. Biol. 11:e1004593 Macromolecular Biochemistry Cell Biology Link

11 publications
Irving JA, Haq I, Dickens JA, Faull SV, Lomas DA (2014) Altered native stability is the dominant basis for susceptibility of α1-antitrypsin mutants to polymerization. Biochemical Journal 460:103–119 Macromolecular Biochemistry Link
James AI, Imran HAQ, Jennifer AD, Sarah VF, David AL (2014) Altered native stability is the dominant basis for susceptibility of alpha1-antitrypsin mutants to polymerization. Biochem. J. 460:103-115 Macromolecular Biochemistry Link
Tunnicliffe RB, Hautbergue GM, Wilson SA, Kalra P, Golovanov AP (2014) Competitive and Cooperative Interactions Mediate RNA Transfer from Herpesvirus Saimiri ORF57 to the Mammalian Export Adaptor ALYREF. PLoS Pathog 10(2): e1003907. Macromolecular Biochemistry Link

3 publications
Firczuk H, Kannambath S, Pahle J, Claydon A, Beynon R, Duncan J, Westerhoff H, Mendes P, McCarthy JEG (2013) An in vivo control map for the eukaryotic mRNA translation machinery. Molecular Systems Biology 9:635 Macromolecular Biochemistry Cell Biology Link
Haq I, Irving JA, Faull SV, Dickens JA, Ordonez A, Belorgey D, Gooptu B, Lomas, DA (2013) Reactive centre loop mutants of alpha-1-antitrypsin reveal position-specific effects on intermediate formation along the polymerization pathway. Biosci. Rep. 33:499-511 Macromolecular Biochemistry Link
Helgeson LA, Nolen BJ (2013) Mechanism of synergistic activation of Arp2/3 complex by cortactin and N-WASP. eLife 2:e00884 Macromolecular Biochemistry Signaling Link
Incicco JJ, Gebhard LG, González-Lebrero RM, Gamarnik AV, Kaufman SB (2013) Steady-State NTPase Activity of Dengue Virus NS3: Number of Catalytic Sites, Nucleotide Specificity and Activation by ssRNA. PLoS ONE 8:e58508 Macromolecular Biochemistry Link
Maccari G, Mori M, Rodríguez-Salarichs J, Fang W, Díaz JF, Botta M (2013) Free Energy Profile and Kinetics Studies of Paclitaxel Internalization from the Outer to the Inner Wall of Microtubules. Journal of Chemical Theory and Computation 9:698-706 Cell Biology Macromolecular Biochemistry Pharmacology Link
Proctor CJ, Boche D, Gray DA, Nicoll JAR (2013) Investigating Interventions in Alzheimer's Disease with Computer Simulation Models. PLoS ONE 8:e73631 Macromolecular Biochemistry Link
Sarma U, Gade PM, Saha B (2013) A mathematical model for dynamics of CD40 clustering. Systems and Synthetic Biol. 7:197-208 Macromolecular Biochemistry Link

7 publications
Chang J-Y, Chantrathammachart P, Monroe DM, Key NS (2012) Studies on the mechanism of action of the aptamer BAX499, an Inhibitor of tissue factor pathway inhibitor. Thrombosis Research 130:e151-e157 Macromolecular Biochemistry Link
Kraut DA, Israeli E, Schrader EK, Patil A, Nakai K, Nanavati D, Inobe T, Matouschek A (2012) Sequence- and Species-Dependence of Proteasomal Processivity. ACS Chemical Biology 7:1444–1453 Biochemistry Macromolecular Biochemistry Link

2 publications
Baez M, Wilson CA, Babul J (2011) Folding kinetic pathway of phosphofructokinase-2 from Escherichia coli: a homodimeric enzyme with a complex domain organization. FEBS Letters 585:2158–2164 Macromolecular Biochemistry Link
Rodriguez F, Bustos MA, Zanetti MN, Ruete MC, Mayorga LS, Tomes CN (2011) alpha-SNAP prevents docking of the acrosome during sperm exocytosis because it sequesters monomeric syntaxin. PLoS ONE 6:e21925 Cell Biology Macromolecular Biochemistry Link

2 publications
Chi CN, Bach A, Gottschalk M, Kristensen AS, Stromgaard K, Jemth P (2010) Deciphering the Kinetic Binding Mechanism of Dimeric Ligands Using a Potent Plasma-stable Dimeric Inhibitor of Postsynaptic Density Protein-95 as an Example. Journal of Biological Chemistry 285:28252–28260 Macromolecular Biochemistry Link
Huang R, Grabarek Z, Wang C-LA (2010) Differential effects of caldesmon on the intermediate conformational states of polymerizing actin. J. Biol. Chem. 285:71-79 Macromolecular Biochemistry Link
Samorodnitsky E, Pugh BF (2010) Genome-Wide Modeling of Transcription Preinitiation Complex Disassembly Mechanisms using ChIP-chip Data. PLoS Comput. Biol. 6:e1000733 Macromolecular Biochemistry Genomics Link

3 publications
Pingoud V, Wende W, Friedhoff P, Reuter M, Alves J, Jeltsch A, Mones L, Fuxreiter M, Pingoud A (2009) On the Divalent Metal Ion Dependence of DNA Cleavage by Restriction Endonucleases of the EcoRI Family. J. Mol. Biol. 393:140-60 Macromolecular Biochemistry Link
Ricagno S, Caccia S, Sorrentino G, Antonini G, Bolognesi M (2009) Human Neuroserpin: Structure and Time-Dependent Inhibition. Journal of Molecular Biology 388:109–121 Enzymology Macromolecular Biochemistry Link

2 publications
Ciocchetta F, Hillston J, Kos M, Tollervey D (2008) Modelling co-transcriptional cleavage in the synthesis of yeast pre-rRNA. Theoretical Computer Science 408:41–54 Macromolecular Biochemistry Link
Kühnel M, Mayorga LS, Dandekar T, Thakar J, Schwarz R, Anes E, Griffiths G, Reich J (2008) Modelling phagosomal lipid networks that regulate actin assembly. BMC Systems Biology 2:107 Metabolism Macromolecular Biochemistry Link
Stefan MI, Edelstein SJ, Le Novère N (2008) An allosteric model of calmodulin explains differential activation of PP2B and CaMKII. PNAS 105:10768-73 Physiology Signaling Macromolecular Biochemistry Link

3 publications
Rippe K, Schrader A, Riede P, Strohner R, Lehmann E,Längst G (2007) DNA sequence- and conformation-directed positioning of nucleosomes by chromatin-remodeling complexes. PNAS 104:15635-40 Macromolecular Biochemistry Cell Biology Link

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