Initial commit with Hugo

.vscode/settings.json

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archetypes/default.md

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config.toml

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+baseURL = "http://example.org/"
+languageCode = "en-us"
+title = "Prof. Dr. Jean-Didier Maréchal's website"
+author = "Jean-Didier Maréchal"

content/_index.md

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+---
+title: Welcome
+menu: "main"
+weight: -10
+---
+
+<div class="content">
+    <header>
+        <h1>Hi, I am Jean-Didier<br />
+        Maréchal</h1>
+        <p>Professor at Universitat Autònoma de Barcelona</p>
+    </header>
+    <p>I am a computational chemist with a wide experience on a broad spectrum of techniques (i.e. from Homology Modeling, MD, QM/MM). My research interests are centered on the computationally aided molecular designs of bioactive molecules and supramolecular complexes. The work performed in my team is mainly dedicated to the development of integrative computational approaches for biomedicinal and biotechnological applications. Our research interests are broad although principally articulated around two main blocks: the study and prediction of drug efficiency and toxicological profiles (ADME and side effects) and the development of artificial enzymes. </p>
+    <p>In these two lines, a substantial amount of efforts is dedicated to metal containing systems. Hence, we are of the leader in simulating metal mediated protein-ligand interactions and eventually subsequent catalytic mechanisms. These interactions have mainly remained orphan of computational inputs so far and their understanding can open major avenues in fields as variables as the fight against Alzheimer disease, erradication of pathogens by iron starvation or the design of environmentally friendly artificial metaloenzymes.</p>
+    <ul class="actions">
+        <li><a href="/research" class="button big">Learn more about my research</a></li>
+    </ul>
+</div>
+<span class="image object">
+    <img src="/images/prot.jpg" alt="Protein" />
+</span>

content/about.md

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+---
+title: About me
+date: 2017-03-23
+publishdate: 2017-03-24
+menu: "main"
+---
+
+Hello!

content/research/_index.md

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+---
+title: Research
+menu: main
+weight: 10
+nav: false
+---
+
+# The Mission
+
+Our mission is to develop and apply molecular modeling tools for the design of pharmacologically or biotechnologically active molecules.
+
+# The Strategy
+
+The computation of complex systems is generally a long shoot. In most of our research, more than one method is needed for an accurate enough prediction. Since feeding molecular modeling programs one to another is of the most tedious and source of errors in computational chemistry, we bet in the development of novel interfaces that combined techniques together and accelerate both the readility of the user and settle novel calculations. In collaboration with the team of the UCSF Chimera package of program, we are implementing novel interface between Homology Modeling, Molecular Dynamics, QM/MM, protein-ligand docking approaches. These novel implementation are key for the exploration of wide chemical and conformational space required for design prospects.
+
+# The Systems
+
+## (Metalo)Drug Design and toxicology
+
+We use our expertise on protein-ligand recognition processes on several biomedicinal problems. One of our particularities is to try to decode the fate of the drugs outside the standard drug-target paradigm. In particular, we are intending to decode off target interactions of anticancer compounds as well as actively work on the development of a computational framework dedicated to the prediction of the metabolism of drugs by cytochromes P450.
+
+## Artificial Enzymes
+
+Biocatalysis aims at generating efficient, enantiospecific and environmentally friendly catalysts in order to surrogate standard organic protocols. The development of novel biocatalysts has therefore become a major focus of attention. We work on several key systems with potential applications in pharmacochemical and agrochemical industries. In particular, we work on artificla metaloenzyms obtained by the insertion of homogeneous catalysts into protein cavities (peroxidases, hydrogenases). Our work provide with important molecular knowledge (determination of the binding of the inorganic moiety, position of the substrate, determination of the transition state, comparison between enantiomeric pathways).
+
+
+## Metalopeptides
+
+At the bridge between both fields previously mentioned, we recently entered in the particular areas of the recognition between metal cations and flexible ligands, more particularly natural or synthetic small size peptides (up to 20 residues). Our results are providing major molecular insights for the design novel molecular scaffold enantioselective peptides as well as contributing to the worldwide effort in the fight against AD.

content/research/item-A.md

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+---
+title: Item A
+date: 2017-03-23
+publishdate: 2017-03-24
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+    main:
+        parent: Research
+weight: 10
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+---

content/research/item-B.md

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+title: Item B
+date: 2017-03-23
+publishdate: 2017-03-24
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+    main:
+        parent: Research
+weight: 10
+nav: false
+---

content/research/item-C.md

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+title: Item C
+date: 2017-03-23
+publishdate: 2017-03-24
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+    main:
+        parent: Research
+weight: 10
+nav: false
+---

content/teaching/appointments.md

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+title: "Appointments & Meetings"
+menu: teaching
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+---
+
+Demo

content/teaching/subjects/_index.md

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content/teaching/subjects/advanced-physical-chemistry.md

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+title: "Chemistry - Advanced Physical Chemistry"
+description: "BLa bla bla "
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content/teaching/subjects/advanced-physical-chemistry/_index.md

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+description: "BLa bla bla "
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content/teaching/subjects/chem4th-biosim.md

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+description: "BLa bla bla "
+menu:
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content/teaching/subjects/chem4th-biosim/_index.md

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+title: "Biomolecular Simulation"
+description: "BLa bla bla"
+menu:
+  teaching:
+    parent: Subjects
+---
+
+
+This is the series of practicum and other interesting material associated to the module "Biomolecular Simulation" of the fourth year of the Chemistry grade of the UAB.

content/teaching/subjects/chem4th-biosim/p1.md

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+---
+title: Practicum 1 - Introduction to Molecular Visualization of Biochemical Systems
+---

content/teaching/subjects/chem4th-biosim/p2.md

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+---
+title: Practicum 2 - Getting used to force field
+---

content/teaching/subjects/chem4th-biosim/p3.md

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+---
+title: Practicum 3 - Protein-Ligand Docking
+---

content/teaching/subjects/chem4th-biosim/p4.md

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+---
+title: Practicum 4 - Molecular Dynamics
+---

content/teaching/subjects/chem4th-biosim/p5.md

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+---
+title: Practicum 5 - QM/MM
+---

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content/teaching/subjects/citeq/p1.md

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content/teaching/subjects/forcefield-qmmm.md

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+menu:
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content/teaching/subjects/forcefield-qmmm/_index.md

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+description: "BLa bla bla "
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content/teaching/subjects/grau-biologia.md

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content/teaching/subjects/grau-biologia/_index.md

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+description: "BLa bla bla "
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content/teaching/subjects/mqtc.md

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content/teaching/subjects/mqtc/_index.md

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content/teaching/subjects/msc-bioinf.md

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+description: "BLa bla bla "
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content/teaching/subjects/msc-bioinf/_index.md

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+description: "BLa bla bla "
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content/teaching/subjects/msc-chem.md

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+description: "BLa bla bla "
+menu:
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content/teaching/subjects/msc-chem/_index.md

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+description: "BLa bla bla "
+menu:
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content/teaching/ucsf-chimera-install.md

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+---
+title: "UCSF Chimera installation in Linux"
+description: "BLa bla bla "
+---
+
+Many of the functions you will be using are experimental or under development. This is the result of our collaboration with the group of San Francisco. So, you may have to install the latest version of the program on your machine (at home or in the classrom). Here is a temptative way of doing so in a step by step process.
+
+1. Download the program ([daily build](https://www.cgl.ucsf.edu/chimera/download.html)). Generally, the downloaded program should be in `~/Baixades` (or `~/Downloads`)
+
+2. Open a terminal (in ubuntu, in the desktop menu, look for `terminal` - konsole or gnome-terminal should appear)
+
+3. In the terminal, go to the directory where the program has been downloaded (i.e. `cd Baixades`)
+
+4. Change the mode of execution of the file: `chmod +x name_chimera_version`
+
+5. Then execute the file: `./name_chimera_version`
+
+6. Press `enter` for all the questions
+
+7. To execute program, go to the directory of installation (i.e. `cd $HOME/.local/UCSF-chimera_version/bin/`)
+
+8. Then execute it: `./chimera`

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