About
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Structural biology is centrally concerned with the description of a biomolecule’s geometry, as angles and distances between the biomolecule’s atoms are measured in order to determine the biomolecular structure. The values of these geometrical parameters may be obtained from biophysical techniques, such as Nuclear Magnetic Resonance spectroscopy. In this PhD project, the performances of a new computational method for protein structure calculation was delved. This method, implemented within the iBPprot software framework, treats protein structure determination as a distance geometry problem, which
the interval branch-&-prune algorithm tries to solve by the full exploration of its solutions space. The results obtained by iBPprot on a set of proteins, with sizes up to 120 residues and displaying various secondary structures and topologies, was analyzed. Using short-range exact distance restraints, it was possible to rebuild the structure of all protein targets, and for many of them it was possible to exhaustively explore their conformational spaces. Because exact distance restraints are not always possible to procure from experimental techniques, the method was then tested with interval data restraints. In this case,iBPprot permitted an exploration of more than 70% of the conformational space size for most of the targets. Furthermore, conformations closer than 5Å to the target conformations were obtained. The quality of the generated structures was satisfactory with respect to Ramachandran plots, but arguable because of the presence of steric clashes in some conformers. The runtime over most performed calculations was competitive with existing structure determination method. |
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Location
Building: Amphithéâtre Jacques Monod, sous-sol bâtiment MONOD 66
Address: 25 Rue du Dr Roux, Paris, France
(function($) {
/*
* render_map
*
* This function will render a Google Map onto the selected jQuery element
*
* @type function
* @date 8/11/2013
* @since 4.3.0
*
* @param $el (jQuery element)
* @return n/a
*/
function render_map( $el ) {
var MY_MAPTYPE_ID = 'custom_style';
var featureOpts = [{"stylers":[{"hue":"#0088ff"}]}];
var styledMapOptions = {
name: 'Custom Style'
};
var customMapType = new google.maps.StyledMapType(featureOpts, styledMapOptions);
// var
var $markers = $el.find('.marker');
// vars
var args = {
zoom : 16,
scrollwheel : false,
center : new google.maps.LatLng(0, 0),
mapTypeId : google.maps.MapTypeId.ROADMAP,
mapTypeId : MY_MAPTYPE_ID
};
// create map
var map = new google.maps.Map( $el[0], args);
map.mapTypes.set(MY_MAPTYPE_ID, customMapType);
// add a markers reference
map.markers = [];
// add markers
$markers.each(function(){
add_marker( $(this), map );
});
// center map
center_map( map );
}
/*
* add_marker
*
* This function will add a marker to the selected Google Map
*
* @type function
* @date 8/11/2013
* @since 4.3.0
*
* @param $marker (jQuery element)
* @param map (Google Map object)
* @return n/a
*/
function add_marker( $marker, map ) {
// var
var latlng = new google.maps.LatLng( $marker.attr('data-lat'), $marker.attr('data-lng') );
//var image = 'https://research.pasteur.fr/wp-content/themes/biologyx2/images/logomap.png';
var myIcon = new google.maps.MarkerImage('https://research.pasteur.fr/wp-content/themes/biologyx2/images/map-pin.png', null, null, null, new google.maps.Size(32,32));
// create marker
var marker = new google.maps.Marker({
position : latlng,
map : map,
icon : myIcon
});
// add to array
map.markers.push( marker );
// if marker contains HTML, add it to an infoWindow
if( $marker.html() )
{
// create info window
var infowindow = new google.maps.InfoWindow({
content : $marker.html()
});
// show info window when marker is clicked
google.maps.event.addListener(marker, 'click', function() {
infowindow.open( map, marker );
});
}
}
/*
* center_map
*
* This function will center the map, showing all markers attached to this map
*
* @type function
* @date 8/11/2013
* @since 4.3.0
*
* @param map (Google Map object)
* @return n/a
*/
function center_map( map ) {
// vars
var bounds = new google.maps.LatLngBounds();
// loop through all markers and create bounds
$.each( map.markers, function( i, marker ){
var latlng = new google.maps.LatLng( marker.position.lat(), marker.position.lng() );
bounds.extend( latlng );
});
// only 1 marker?
if( map.markers.length == 1 )
{
// set center of map
map.setCenter( bounds.getCenter() );
map.setZoom( 15 );
}
else
{
// fit to bounds
map.fitBounds( bounds );
}
}
/*
* document ready
*
* This function will render each map when the document is ready (page has loaded)
*
* @type function
* @date 8/11/2013
* @since 5.0.0
*
* @param n/a
* @return n/a
*/
$(document).ready(function(){
$('.acf-map').each(function(){
render_map( $(this) );
});
});
})(jQuery);
