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The last changes I did to new
JeanDidier Oct 27, 2016
5b4fa2c
Fix unnecessary br tags, disabled link to gaudi page since it's not y…
jaimergp Oct 28, 2016
8f7eee1
Ignore .* files
jaimergp Oct 28, 2016
6c8094d
Ignore .* files - deletion
jaimergp Oct 28, 2016
a2c869f
Merge branch 'master' into updates_JD
JeanDidier Nov 3, 2016
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3 changes: 2 additions & 1 deletion .gitignore
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124 changes: 124 additions & 0 deletions gaudi.html
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<!DOCTYPE HTML>
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<h1><a href="#">InsiliChem</a></h1>
<p>Molecular Modeling for study and design of<br />
<strong>chemobiotechnological systems</strong></p>
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<h2>GAUDI</h2>
<p>In construction</p>

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<li><span class="icon icon-flask"><span class="label">Chemistry</span></span></li>
<li><span class="icon icon-leaf"><span class="label">Biotech</span></span></li>
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<h3>The underlying idea</h3>
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<h3>The Problem </h3>

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<p class="fit">
<strong>InsiliChem</strong><br />
Molecular Modeling of Transition Metal Systems<br />
Unitat de Química-Física, Department de Química<br />
Facultat de Ciències, Universitat Autònoma de Barcelona<br />
Barcelona, Spain
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25 changes: 17 additions & 8 deletions index.html
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Expand Up @@ -42,13 +42,20 @@ <h1><a href="#">InsiliChem</a></h1>
<!-- One -->
<section id="about" class="wrapper style2 special">
<header class="major inner">
<h2>We are a young team of molecular modelers</h2>

<p>Led by Dr. Jean-Didier Maréchal, our group focuses on the modeling of systems at the interface between <strong> chemistry and biology</strong>. Our primary interests are chemobiological hybrids like artificial enzymes, biosensors and biomarkers and more particularly those involving transition metal moeties. We have a large network of collaborations worldwide both with experimental and theoretical groups leader in these fields.<br/><br/>
We also intensively work on <strong> structural bioinformatics and computational chemistry methodological developments </strong> that could sustain our investigation and our <strong>multi-scale procedures</strong>. Most of our efforts are performed using <strong>Python</strong> as a principal scripting language.<br/><br/>
<strong>InsiliChem</strong> is part of Professor Agustí Lledós laboratory of <em>Molecular Modeling of Transition Metal Systems</em> located at the Chemistry Department of the Universitat Autònoma de Barcelona (Spain). </p>
<h2>Multi-Scale and Novel Computational Strategies for Complex Modeling</h2>
<p>
Led by Dr. Jean-Didier Maréchal, the activity of <strong>InsiliChem</strong> focuses on the modeling and design of <strong>molecular systems</strong>. We work on a broad range of applications in the <strong>chemical biology </strong> and <strong>supramolecular chemistry</strong> areas. One of our particular field of expertise is the study of <strong> chemobiological hybrids </strong> like artificial enzymes, biosensors and biomarkers that stand on complementarities between biomolecules and transition metal moeties. </p>
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Our research stands on <strong>2 major computational components</strong>. One is the <strong>integrative</strong> use of different level of theory and the optimization of the intercommunication between the software that sustain them. This <strong> Multi-Level framework</strong> offers us major opportunities in working on complex systems. The other is a series of <strong>novel computational tools </strong> that bridge standard explorative procedures, like Genetic Algorithms, with <strong> conditional modeling </strong> hence bridging <strong> (biophys)chemical intuition</strong> in the exploration of wide biochemical spaces. Most of our developments are performed using <strong>Python</strong> as a principal scripting language.
</p>
<p>
<strong>InsiliChem</strong> is part of Professor Agustí Lledós laboratory of <em>Molecular Modeling of Transition Metal Systems</em> located at the Chemistry Department of the Universitat Autònoma de Barcelona (Spain). Added to excellent installation, we have a large network of collaborations worldwide both with experimental and theoretical groups leader in these fields.
</p>
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<ul class="inner icons major">
<li><span class="icon icon-flask"><span class="label">Chemistry</span></span></li>
<li><span class="icon icon-leaf"><span class="label">Biotech</span></span></li>
<li><span class="icon icon-uniF153"><span class="label">Python</span></span></li>
Expand Down Expand Up @@ -79,8 +86,10 @@ <h3>The Strategy</h3>
<h3>The Tools</h3>
<p>Our software developments are centred on two axis: </p>
<ol>
<li><p>To accelerate our multiscale studies, we develop software and interfaces that could ease management of input and output files. In collaboration with the team of the UCSF Chimera, we are implementing novel interface between Homology Modeling, Molecular Dynamics, QM/MM, protein-ligand docking approaches.</p></li>
<li>Most of our work also involve major exploration of chemical and conformational space. As current state-of-the-art programs do not consider both exploration spaces, we are intensively working on a genetic algorithm based architecture for this end. </li>
<li><p>To accelerate our multiscale studies, we develop software and interfaces that could ease management of input and output files. In collaboration with the team of the UCSF Chimera, we are implementing novel interface between Homology Modeling, Molecular Dynamics, QM/MM, protein-ligand docking approaches.
<a href="multiscale.html#plumme" class="button icon icon-briefcase" target="_blank" style="margin-top: 1em">More on our platform PluMMe here</a></p></li>

<li><p>Most of our work also involve major exploration of chemical and conformational space. As current state-of-the-art programs do not consider both exploration spaces, we are intensively working on a genetic algorithm based architecture for this end.<a class="button icon icon-briefcase" style="margin-top: 1em">More on our platform GAUDI coming soon</a></p></li>
</ol>
</div>
</section>
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132 changes: 132 additions & 0 deletions multiscale.html
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<!DOCTYPE HTML>
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-->
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<!-- Header -->
<header id="header">
<div class="content">
<h1><a href="#">InsiliChem</a></h1>
<p>Molecular Modeling for study and design of<br />
<strong>chemobiotechnological systems</strong></p>
<ul class="actions">
<li><a href="#about" class="button icon icon-info scrolly">About us</a></li>
<li><a href="https://github.com/insilichem" class="button icon icon-github">Repository</a></li>
<li><a href="#contact" class="button icon icon-angle-down scrolly">Contact</a></li>
</ul>
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<li><a href="#opportunities" class="button special icon icon-briefcase scrolly">Open positions</a></li>
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<section id="plumme" class="wrapper style2 special">
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<h2>PluMMe: A Multi-Scale Plateform </h2>

<p>In the recent years, InsiliChem has been involved in the development of a multiscale platform which has been recently named as PluMMe for Python Layer for Unified Molecular ModEling.</p></br></br>



</header>
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<li><span class="icon icon-flask"><span class="label">Chemistry</span></span></li>
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<h3>The underlying idea</h3>
<p>Bridging several modelling methods together is now a common strategy in computational chemistry and are generally referred as Multi-Scale methods. These combinations could have different level of complexities. One of the most frequent is a “simple” two step procedure where one method of low accuracy level is used to explore wide conformational space (i.e. Force Field Molecular Dynamics) and a second, of higher quality, is performed on a series of eligible candidates (i.e. QM/MM refinement). On the other extremity the spectrum, complex multi-scale modelling may be reached with many different methods combined in hierarchical, integrative, sequential or even iterative manner. In these types of methodologies the data go from one level of theory to another in order to get convenient energetic and structural features of complex systems. </p>
</div>
</section>

<section class="spotlight">
<div class="image"><img src="images/multiscale.jpg" alt="" /></div>
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<h3>The Problem </h3>
<p>If articulating several methods constitutes the cornerstone of many computational chemistry studies, multi-scale modelling has not yet reach a conventional way to proceed. There are a series of methodological and technical complexities. One particular bottleneck in the Multi-Scale landscape is the optimization of input/output data flow between different software. Intercommunication between software is never a priority for standalone programs and generally modellers spend a substantial amount of time and distress on getting the correct transformation of an output result into a input for the execution of a new calculation. With the huge potential that offers multi-scale modelling in the future of chemical sciences and more particularly for chemical applications at interfacial sciences like bio- or nanotechnologies, providing with easy going and generalist user interfaces that could be easily adapted from software to software would represent a major step forward. </p>
</div>
</section>

<section class="spotlight">
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<h3>The PluMMe package</h3>
<p>Since feeding molecular modeling programs from one to another is of the most tedious and source of errors in computational chemistry, we and others are betting on multiscale/integrative/multilevel approaches that conveniently combine in a unique protocol by developping interfaces that do not alter the internal code of each software of the pipeline but transform only input and output is a effective way.</p>
<p>A substentially amount of interfaces have been created yet and stand on UCSF Chimera facilities. In writting process at the moment, PluMMe will soon be available for download.</p>

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<p class="fit">
<strong>InsiliChem</strong><br />
Molecular Modeling of Transition Metal Systems<br />
Unitat de Química-Física, Department de Química<br />
Facultat de Ciències, Universitat Autònoma de Barcelona<br />
Barcelona, Spain
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