psychoprot.epfl.ch
Alignments --> Variability matrix
http://psychoprot.epfl.ch/aln2data.html
Create amino acid variability matrix from alignment of protein sequences. This tool computes ΔΔG and k* from an alignment of protein sequences and compiles a table with all the data. Additionally, it adds a parameter that measures the involvement of each residue in contacts relevant for the protein's structure, if the couplings computed by EVFold or EVCouplings. Paste your alignment and optionally your coevolution data below and click Run. Marks and Sander groups) and Gremlin. ALIGNMENT: Load from file:.
psychoprot.epfl.ch
Loading program
http://psychoprot.epfl.ch/fits_from_ddg_data.html
PsychoProt: Physical CHemistry Of Protein variability. A tool to fit amino acid variability data to physicochemical descriptors (know more.). Help on the data format. Here's a tool to build the data table from an alignment. Paste below or Load from:. Set parameters and click "Analyze". K* values (= effective number of tolerated amino acids). Additional column with numeric data to plot. Criteria for Fit Selection:. Rec 001 - 0.05. Filter also by Root Mean Square. Error and Pearson coefficient. Hint: Use a...
vdg.epfl.ch
Bacterial Pore-Forming Toxins | VDG
http://vdg.epfl.ch/PoreFormingToxins
Jump to search field. Van der Goot Lab. School of Life Sciences. Van der Goot Lab. Van der Goot Lab. Compartmentalization of Mammalian Cells and Cell Membranes. How to reach us? Pore-forming toxins have been the longest standing interest of the group. In an intense collaboration with the groups of Matteo Dal Peraro. As well as groups in non-SV EPFL Faculty ( Philippe Renaud. Paolo de los Rios. We are studying the conformational changes and assembly of pathways involved in the pore-formation process.
vdg.epfl.ch
Compartmentalization of Mammalian Cells and Cell Membranes | VDG
http://vdg.epfl.ch/cms/site/vdg/lang/en/Compartmentalization
Jump to search field. Van der Goot Lab. School of Life Sciences. Van der Goot Lab. Compartmentalization of Mammalian Cells and Cell Membranes. Van der Goot Lab. Compartmentalization of Mammalian Cells and Cell Membranes. How to reach us? Compartmentalization of Mammalian Cells and Cell Membranes. Compartmentalization of Mammalian Cells and Cell Membranes. Compartmentalization of Mammalian Cells and Cell Membranes. The group has had a longstanding interest in the 2D compartmental. Top of the page.
vdg.epfl.ch
Compartmentalization of Mammalian Cells and Cell Membranes | VDG
http://vdg.epfl.ch/Compartmentalization
Jump to search field. Van der Goot Lab. School of Life Sciences. Van der Goot Lab. Compartmentalization of Mammalian Cells and Cell Membranes. Van der Goot Lab. Compartmentalization of Mammalian Cells and Cell Membranes. How to reach us? Compartmentalization of Mammalian Cells and Cell Membranes. Compartmentalization of Mammalian Cells and Cell Membranes. Compartmentalization of Mammalian Cells and Cell Membranes. The group has had a longstanding interest in the 2D compartmental. Top of the page.
vdg.epfl.ch
Bacterial Pore-Forming Toxins | VDG
http://vdg.epfl.ch/cms/site/vdg/lang/en/PoreFormingToxins
Jump to search field. Van der Goot Lab. School of Life Sciences. Van der Goot Lab. Van der Goot Lab. Compartmentalization of Mammalian Cells and Cell Membranes. How to reach us? Pore-forming toxins have been the longest standing interest of the group. In an intense collaboration with the groups of Matteo Dal Peraro. As well as groups in non-SV EPFL Faculty ( Philippe Renaud. Paolo de los Rios. We are studying the conformational changes and assembly of pathways involved in the pore-formation process.
lipidbuilder.epfl.ch
References | Lipid builder
http://lipidbuilder.epfl.ch/references
RM Venable, A.J. Sodt, B. Rogaski, H. Rui, E. Hatcher, A.D. MacKerell, Jr., R.W. Pastor, and J.B. Klauda,CHARMM all-atom additive force field for sphingomyelin: elucidation of hydrogen bonding and of positive curvature, Biophys J. T Lemmin*, C. Bovigny*, D. Lancon and M. Dal Peraro, Cardiolipin Models for Molecular Simulations of Bacterial and Mitochondrial Membranes, Journal of Chemical Theory and Computation. GGA Software Services LLC - Ketcher. Sam Stephenson - Prototype. Roland Franssen - Dialog.
lipidbuilder.epfl.ch
VMD plugin | Lipid builder
http://lipidbuilder.epfl.ch/plugin
Download LipidBuilder Plugin v3.0. Add the following to $HOME/.vmdrc. Vmd install extension lipidBuilder lipidbuilder tk "Modeling/LipidBuild. Export Smiles ChemDraw or other softwares. Fill the GUI formular of Lipid Builder Plugin. Creative Commons CC BY-SA 3.0. License. LBM EPFL.
lipidbuilder.epfl.ch
Home | Lipid builder
http://lipidbuilder.epfl.ch/demo
The physicochemical properties of the different lipid species are essential for the structural and functional organization of the biological membrane and its interaction with integral and peripheral membrane proteins. The lipid head groups are not the only important determinants of membranes; the nature of the lipid acyl chains strongly influences membrane properties. To facilitate the creation of realistic biological membranes for molecular simulations, the present web-server, based on a VMD.
lipidbuilder.epfl.ch
Builder | Lipid builder
http://lipidbuilder.epfl.ch/builder
LipidBuilder automatically generates the topology and template of a given lipid. The lipid topology is created by combining the selected head group, extracted from a built-in library of structures and the provided hydrocarbon chains. Four different classes of hydrocarbons have been parametrized in the CHARMM force field: saturated, unsaturated, branched and cyclopropane. How to build a Lipid? Choose a lipid head. Click on Build lipid. To preview the lipid. Click on the Save to library. Choose a head group.
