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Detecting micro domains in model membranes with APL@VORO

1/26/2015

224 Comments

 
APL@Voro is a program developed to aid in the analysis of Molecular dynamics trajectories of lipid bilayer simulations. Initially designed to work with GROMACS trajectory files, it may be used also with other trajectories if they are converted to Gromacs format (needed are the Gromacs trajectory file, PDB coordinate files and a GROMACS index files) to create a two dimensional geometric representation of a bilayer. The analysis of the bilayer is supported by using the Voronoi diagrams and Delaunay triangulations generated for different selection models of lipids. The values calculated on the geometric structures can be visualized in an interactive environment, plotted and exported to different file types. APL@Voro supports complex bilayers with a mix of various lipids and proteins and calculates the area per lipid and the bilayer thickness. The program is written in C++, open source and published under the GPL 3.0 License.

Download the software here.


For the algorithms used click here.

224 Comments

SQUEEZE-E: How to make a simulation cell based on the shape of the molecule

10/11/2013

0 Comments

 
Read below on how the authors below made a method to define a box which is based on the shape of the molecule. This should drastically recude the number of atoms and hence simulation time! i(if the rotation is constrained)

SQUEEZE-E: The Optimal Solution for Molecular Simulations with Periodic Boundary Conditions
b
y Tsjerk A. Wassenaar *†‡, Sjoerd de Vries ‡, Alexandre M. J. J. Bonvin ‡, and Henk Bekker §

In molecular simulations of macromolecules, it is desirable to limit the amount of solvent in the system to avoid spending computational resources on uninteresting solvent–solvent interactions. As a consequence, periodic boundary conditions are commonly used, with a simulation box chosen as small as possible, for a given minimal distance between images. Here, we describe how such a simulation cell can be set up for ensembles, taking into account a priori available or estimable information regarding conformational flexibility. Doing so ensures that any conformation present in the input ensemble will satisfy the distance criterion during the simulation. This helps avoid periodicity artifacts due to conformational changes. The method introduces three new approaches in computational geometry: (1) The first is the derivation of an optimal packing of ensembles, for which the mathematical framework is described. (2) A new method for approximating the α-hull and the contact body for single bodies and ensembles is presented, which is orders of magnitude faster than existing routines, allowing the calculation of packings of large ensembles and/or large bodies. 3. A routine is described for searching a combination of three vectors on a discretized contact body forming a reduced base for a lattice with minimal cell volume. The new algorithms reduce the time required to calculate packings of single bodies from minutes or hours to seconds. The use and efficacy of the method is demonstrated for ensembles obtained from NMR, MD simulations, and elastic network modeling. An implementation of the method has been made available online at http://haddock.chem.uu.nl/services/SQUEEZE/ and has been made available as an option for running simulations through the weNMR GRID MD server at http://haddock.science.uu.nl/enmr/services/GROMACS/main.php.
0 Comments

Computational Drug Discovery and Design volume from @SpringerPub

3/1/2013

1 Comment

 
Riccardo Baron also put together a great computational methods volume you should have access to:http://link.springer.com/book/10.1007/978-1-61779-465-0/page/1
Here's the list of contents:

Drug Binding Site Prediction, Design, and Descriptors
A Molecular Dynamics Ensemble-Based Approach for the Mapping of Druggable Binding Sites
  • Anthony Ivetac, J. Andrew McCammon Look Inside Get Access
Analysis of Protein Binding Sites by Computational Solvent Mapping
  • David R. Hall, Dima Kozakov, Sandor Vajda
Evolutionary Trace for Prediction and Redesign of Protein Functional Sites
  • Angela Wilkins,Serkan Erdin,Rhonald Lua,Olivier Lichtarge
Information Entropic Functions for Molecular Descriptor Profiling
  • Anne Mai Wassermann,Britta Nisius,Martin Vogt,Jürgen Bajorath

Virtual Screening of Large Compound Libraries: Including Molecular Flexibility
Expanding the Conformational Selection Paradigm in Protein-Ligand Docking
  • Guray Kuzu,Ozlem Keskin,Attila Gursoy,Ruth Nussinov Look Inside Get Access
Flexibility Analysis of Biomacromolecules with Application to Computer-Aided Drug Design
  • Simone Fulle,Holger Gohlke
On the Use of Molecular Dynamics Receptor Conformations for Virtual Screening
  • Sara E. Nichols,Riccardo Baron,J. Andrew McCammon
Virtual Ligand Screening Against Comparative Protein Structure Models
  • Hao Fan,John J. Irwin,Andrej Sali
AMMOS Software: Method and Application
  • T. Pencheva,D. Lagorce,I. Pajeva,B. O. Villoutreix,M. A. Miteva
Rosetta Ligand Docking with Flexible XML Protocols
  • Gordon Lemmon,Jens Meiler
Normal Mode-Based Approaches in Receptor Ensemble Docking
  • Claudio N. Cavasotto
Application of Conformational Clustering in Protein–Ligand Docking
  • Giovanni Bottegoni,Walter Rocchia,Andrea Cavalli
How to Benchmark Methods for Structure-Based Virtual Screening of Large Compound Libraries
  • Andrew J. Christofferson,Niu Huang

Prediction of Protein-Protein Docking and Interactions

AGGRESCAN: Method, Application, and Perspectives for Drug Design
  • Natalia S. de Groot,Virginia Castillo,Ricardo Graña-Montes,Salvador Ventura
ATTRACT and PTOOLS: Open Source Programs for Protein–Protein Docking
  • Sebastian Schneider,Adrien Saladin,Sébastien Fiorucci,Chantal Prévost
Prediction of Interacting Protein Residues Using Sequence and Structure Data
  • Vedran Franke,Mile Šikić,Kristian Vlahoviček

Rescoring Docking Predictions
MM-GB/SA Rescoring of Docking Poses
  • Cristiano R. W. Guimarães
A Case Study of Scoring and Rescoring in Peptide Docking
  • Zunnan Huang, Chung F. Wong
The Solvated Interaction Energy Method for Scoring Binding Affinities
  • Traian Sulea, Enrico O. Purisima
Linear Interaction Energy: Method and Applications in Drug Design
  • Hugo Gutiérrez-de-Terán, Johan Åqvist 
1 Comment

Analysis of MD simulations using GROMACS tools

11/7/2012

5 Comments

 
I just came across this presentation which very nicely summarises the most important analysis tools for proteins available in Gromacs:  Definitely worth reading and very good as a reference for experienced gromacs users.

Analysis tools that you can find in the presentation include:
- Looking at your trajectory
- Groups in analysis
- Root mean square deviations and fluctuations
- Radius of gyration and distances
- Hydrogen bonds
- Secondary structure analysis
- Free energy surfaces
- Principal component analysis: using Cartesian coordinates or dihedral angles
- Clustering

Evi


5 Comments

    Alexis, Michalis, Danai, Panos, Sotiris, Nastazia, Vassilis, Zoe

    lab group members!

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