Browsing by Subject "Computational Biology"

Article

CHARMM: The biomolecular simulation program

Brooks, B. R.; Brooks III, C. L.; Mackerell Jr., A. D.; Nilsson, L.; Petrella, R. J.; Roux, B.; Won, Y.; Archontis, Georgios Z.; Bartels, C.; Boresch, S.; Caflisch, A.; Caves, L.; Cui, Q.; Dinner, A. R.; Feig, M.; Fischer, S.; Gao, J.; Hodoscek, M.; Im, W.; Kuczera, K.; Lazaridis, T.; Ma, J.; Ovchinnikov, V.; Paci, E.; Pastor, R. W.; Post, C. B.; Pu, J. Z.; Schaefer, M.; Tidor, B.; Venable, R. M.; Woodcock, H. L.; Wu, X.; Yang, W.; York, D. M.; Karplus, M. (2009)

CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and widely used molecular simulation program. It has been developed over the last three decades with a primary focus on molecules of biological interest, ...

Article

Computational protein design with a generalized born solvent model: Application to asparaginyl-tRNA synthetase

Polydorides, Savvas; Amara, Najette; Aubard, C.; Plateau, P.; Simonson, T.; Archontis, Georgios Z. (2011)

Computational Protein Design (CPD) is a promising method for high throughput protein and ligand mutagenesis. Recently, we developed a CPD method that used a polar-hydrogen energy function for protein interactions and a ...

Article

Computational protein design: The proteus software and selected applications

Simonson, T.; Gaillard, T.; Mignon, D.; Schmidt Am Busch, M.; Lopes, A.; Amara, Najette; Polydorides, Savvas; Sedano, A.; Druart, Karen; Archontis, Georgios Z. (2013)

We describe an automated procedure for protein design, implemented in a flexible software package, called Proteus. System setup and calculation of an energy matrix are done with the XPLOR modeling program and its sophisticated ...

Article

A computationally fast measure of epistasis for 2 SNPs and a categorical phenotype.

Antoniades, Athos; Matthews, P. M.; Pattichis, Constantinos S.; Galwey, N. W. (2010)

Complex diseases may be caused by interactions or combined effects between multiple genetic and environmental factors. One of the main limitations of testing for interaction between genetic loci in large whole genome studies ...

Article

Crystallographic and computational studies on 4-phenyl-N-(β-D- glucopyranosyl)-1H-1,2, 3-triazole-1-acetamide, an inhibitor of glycogen phosphorylase: Comparison with α-D-glucose, N-acetyl-β-D- glucopyranosylamine and N-benzoyl-N′-β-D-glucopyranosyl urea binding

Alexacou, Kyra Melinda; Hayes, Joseph M.; Tiraidis, Costas; Zographos, Spyros E.; Leonidas, Demetres D.; Chrysina, Evangelia D.; Archontis, Georgios Z.; Oikonomakos, Nikos G.; Paul, J. V.; Varghese, B.; Loganathan, D. (2008)

4-Phenyl-N-(β-D-glucopyranosyl)-1H-1,2,3-triazole-1-acetamide (glucosyltriazolylacetamide) has been studied in kinetic and crystallographic experiments with glycogen phosphorylase b (GPb), in an effort to utilize its ...

Article

FOXO3a is broadly neuroprotective in vitro and in vivo against insults implicated in motor neuron diseases

Mojsilovic-Petrovic, J.; Nedelsky, N.; Boccitto, M.; Mano, I.; Georgiades, Savvas N.; Zhou, W.; Liu, Y.; Neve, R. L.; Taylor, J. P.; Driscoll, M.; Clardy, J.; Merry, D.; Kalb, R. G. (2009)

Aging is a risk factor for the development of adult-onset neurodegenerative diseases. Although some of the molecular pathways regulating longevity and stress resistance in lower organisms are defined (i.e., those activating ...

Article

Guest editorial introduction to the special issue on citizen centered e-health systems in a global healthcare environment: Selected papers from ITAB 2009

Pattichis, Constantinos S.; Schizas, Christos N.; Kyriacou, Efthyvoulos C.; Fotiadis, Dimitrios Ioannis; Pattichis, Marios S.; Bamidis, Panagiotis D. (2011)

The January 2011 Special Issue of IEEE Transactions on Information Technology in Biomedicine includes selected papers from Information Technology in Biomedicine (ITAB 2009), held in the month of October in Cyprus. The ...

Article

Guest editorial: Introduction to the special section on biomedical informatics

Fotiadis, Dimitrios Ioannis; Pattichis, Constantinos S. (2009)

Article

Guest editorial: Introduction to the special section on computational intelligence in medical systems

Pattichis, Constantinos S.; Schizas, Christos N.; Pattichis, Marios S.; Micheli-Tzanakou, Litsa Evangelia; Kyriacou, Efthyvoulos C.; Fotiadis, Dimitrios Ioannis (2009)

Article

Increased number of MicroRNA target sites in genes encoded in CNV regions. Evidence for an evolutionary genomic interaction

Felekkis, Kyriacos N.; Voskarides, Konstantinos; Dweep, H.; Sticht, C.; Gretz, N.; Constantinou-Deltas, Constantinos D. (2011)

MicroRNAs (miRNAs) and copy number variations (CNVs) are two newly discovered genetic elements that have revolutionized the field of molecular biology and genetics. By performing in silico whole genome analysis, we demonstrate ...

Article

Learning optimisation by high firing irregularity

Cleanthous, A.; Christodoulou, Chris C. (2012)

In a network of leaky integrate-and-fire (LIF) neurons, we investigate the functional role of irregular spiking at high rates. Irregular spiking is produced by either employing the partial somatic reset mechanism on every ...

Article

The pathogenic properties of a novel and conserved gene product, KerV, in proteobacteria

An, D.; Apidianakis, Yiorgos; Boechat, A. L.; Baldini, R. L.; Goumnerov, B. C.; Rahme, L. G. (2009)

Identification of novel virulence factors is essential for understanding bacterial pathogenesis and designing antibacterial strategies. In this study, we uncover such a factor, termed KerV, in Proteobacteria. Experiments ...

Article

Synthesis, structural characterization and in vitro inhibitory studies against human breast cancer of the bis-(2,6-di-tert-butylphenol)tin(iv) dichloride and its complexes

Shpakovsky, D. B.; Banti, Christina N.; Beaulieu-Houle, G.; Kourkoumelis, Nikolaos; Manoli, Maria; Manos, Manolis J.; Tasiopoulos, Anastasios J.; Hadjikakou, Sotiris K.; Milaeva, E. R.; Charalabopoulos, Konstantinos A.; Bakas, Thomas V.; Butler, I. S.; Hadjiliadis, Nick (2012)

Four new organotin(iv) complexes of bis-(2,6-di-tert-butylphenol)tin(iv) dichloride [(tert-Bu-)2(HO-Ph)]2SnCl2 (1) with the heterocyclic thioamides 2-mercapto-pyrimidine (PMTH), 2-mercapto-4-methyl- pyrimidine (MPMTH), ...