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Software produced within our team
We currently have a few open source software released to the public.
They are listed hereafter in reverse chronological order.
EdaFold is a C++/MPI software prototype for fragment-based
protein structure prediction based on an Estimation of
Distribution Algorithm. Fragment-based approaches
build protein models by assembling short fragments
from known protein structures. Whereas the probability mass functions
over the fragment libraries are uniform in the
usual case, we propose an algorithm that learns from previously
generated decoys and steers the search towards native-like regions.
The corresponding
article.
Durandal is a tool implementing entropy-accelerated exact clustering
for protein models stored in PDB files.
Clustering is commonly used to identify the best decoy
among many generated in protein structure prediction when using
energy alone is insufficient. Calculation of the pairwise distance
matrix for a large decoy set is computationally expensive. Typically,
only a reduced set of decoys using energy filtering is subjected to
clustering analysis. We propose a method using propagation of geometric
constraints to accelerate exact clustering, without compromising the
distance measure. Our method can be used with any metric distance.
The corresponding
article.
PAR is a PARallel and distributed job crusher. Bag-of-Tasks (BoT)
applications are commonly encountered in bioinformatics. They consist of a
large number of independent computation-intensive tasks. PAR is a scalable,
dynamic, parallel and distributed execution engine for Bag-of-Tasks.
PAR is aimed at multi-core architectures and small clusters.
The corresponding
article.
MORPHEUS
MORPHEUS is a tool to identify and rebuild residues in predicted models with a large error. The error in predicted models is estimated using the average pairwise geometric distance per residue computed among selected lowest energy models. This error distribution among residues is employed to guide the rebuilding process that focuses on more error-prone residues of the coarse-grain models. MORPHEUS is implemented in C++. It can be run either in batch mode or in parallel mode using MPI. The corresponding article.EdaFold
EdaFold is a C++/MPI software prototype for fragment-based
protein structure prediction based on an Estimation of
Distribution Algorithm. Fragment-based approaches
build protein models by assembling short fragments
from known protein structures. Whereas the probability mass functions
over the fragment libraries are uniform in the
usual case, we propose an algorithm that learns from previously
generated decoys and steers the search towards native-like regions.
The corresponding
article.
Durandal with QCP
We have further enhanced the performance of Durandal by incorporating a Quaternion-based Characteristic Polynomial (QCP) method to speedup RMSD calculations. The corresponding article.Durandal
Durandal is a tool implementing entropy-accelerated exact clustering
for protein models stored in PDB files.
Clustering is commonly used to identify the best decoy
among many generated in protein structure prediction when using
energy alone is insufficient. Calculation of the pairwise distance
matrix for a large decoy set is computationally expensive. Typically,
only a reduced set of decoys using energy filtering is subjected to
clustering analysis. We propose a method using propagation of geometric
constraints to accelerate exact clustering, without compromising the
distance measure. Our method can be used with any metric distance.
The corresponding
article.
Durandal became an official Phenix tool, starting from Phenix v.1.7.2 !
PAR
PAR is a PARallel and distributed job crusher. Bag-of-Tasks (BoT)
applications are commonly encountered in bioinformatics. They consist of a
large number of independent computation-intensive tasks. PAR is a scalable,
dynamic, parallel and distributed execution engine for Bag-of-Tasks.
PAR is aimed at multi-core architectures and small clusters.
The corresponding
article.