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Biarnes X.,Institute Quimic Of Sarria Iqs | Biarnes X.,International School for Advanced Studies | Pietrucci F.,Ecole Polytechnique Federale de Lausanne | Marinelli F.,Max Planck Institute of Biophysics | Laio A.,International School for Advanced Studies
Computer Physics Communications | Year: 2012

We present a new computational tool, METAGUI, which extends the VMD program with a graphical user interface that allows constructing a thermodynamic and kinetic model of a given process simulated by large-scale molecular dynamics. The tool is specially designed for analyzing metadynamics based simulations. The huge amount of diverse structures generated during such a simulation is partitioned into a set of microstates (i.e. structures with similar values of the collective variables). Their relative free energies are then computed by a weighted-histogram procedure and the most relevant free energy wells are identified by diagonalization of the rate matrix followed by a commitor analysis. All this procedure leads to a convenient representation of the metastable states and long-time kinetics of the system which can be compared with experimental data. The tool allows to seamlessly switch between a collective variables space representation of microstates and their atomic structure representation, which greatly facilitates the set-up and analysis of molecular dynamics simulations. METAGUI is based on the output format of the PLUMED plugin, making it compatible with a number of different molecular dynamics packages like AMBER, NAMD, GROMACS and several others. The METAGUI source files can be downloaded from the PLUMED web site (http://www.plumed-code. org). © 2011 Elsevier B.V. All rights reserved. Source


Athanasakis E.,Institute for Maternal and Child Health | Biarnes X.,Institute Quimic Of Sarria Iqs | Bonati M.T.,Clinic of Medical genetics | Gasparini P.,Institute for Maternal and Child Health | Faletra F.,Institute for Maternal and Child Health
Molecular Syndromology | Year: 2012

Proximal symphalangism (SYM1) is a joint morphogenesis disorder characterized by stapes ankylosis, proximal interphalangeal joint fusion, skeletal anomalies and conductive hearing loss. Noggin is a bone morphogenetic protein (BMP) antagonist essential for normal bone and joint development in humans and mice. Autosomal dominant mutations have been described in the NOG gene, encoding the noggin protein. We analyzed an Italian sporadic patient with SYM1 due to a novel NOG mutation (L46P) based on a c.137T>C transition. A different pathogenic mutation in the same codon (L46D) has been previously described in an in vivo chicken model. An in silico model shows a decreased binding affinity between noggin and BMP7 for both L46D and L46P compared to the wild type. Therefore, this codon should play an important role in BMP7 binding activity of the noggin protein and consequently to the joint morphogenesis. Copyright © 2012 S. Karger AG. Source


Balfagon A.C.,Institute Quimic Of Sarria Iqs | Serrano-Hernanz A.,Institute Quimic Of Sarria Iqs | Teixido J.,Institute Quimic Of Sarria Iqs | Tejedor-Estrada R.,Institute Quimic Of Sarria Iqs
International Journal of Cosmetic Science | Year: 2010

In this work, a comparative study between two methods to acquire relevant information about a cosmetic formulation has been carried out. A Design of Experiments (DOE) has been applied in two stages to a capillary cosmetic cream: first, a Plackett-Burman (PB) design has been used to reduce the number of variables to be studied; second, a complete factorial design has been implemented. With the experimental data collected from the DOE, a Least Mean Square (LMS) algorithm and Artificial Neural Networks (ANN) have been utilized to obtain an equation (or model) that could explain cream viscosity. Calculations have shown that ANN are the best prediction method to fit a model to experimental data, within the interval of concentrations defined by the whole set of experiments. © 2010 Society of Cosmetic Scientists and the Société Française de Cosmétologie. Source

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