TMFree: A Compiler Mechanism to Elide Unnecessary Barriers in Transactional Memory Code
TMFree is a compiler mechanism implemented in LLVM that allows programmers to precisely identify and...
MDLovoFit: Automatic identification of mobile and rigid substructure in protein dynamics
MDLovoFit is a package for the analysis of the mobility and structural fluctuation in Molecular...
TopoLink: A package to evaluate structural models using chemical crosslinking distance constraints.
TOPOLINK is a package to compute topological distances between atoms on the surface of proteins...
CellListMap.jl: Efficient and customizable cell list implementation for calculation of pairwise particle properties within a cutoff
L. Martínez, CellListMap.jl: Efficient and customizable cell list implementation for calculation of pairwise particle properties...
OmpCloud: Programming Cloud Clusters with OpenMP
OmpCloud is a toolset that allows you to use the cloud as an OpenMP offloading...
LovoAlign: General molecular structural alignment package
LovoAlign is a new protein structural alignment package. The methods used for structural alignment are...
PGA: a Polyploid Gene Assembler
PGA was developed using PERL scripts for running in Linux system and integrates various software...
MassCCS: Massive Collision Cross Section calculations for large macromolecular assemblies
This repository contains a set of source codes and input scripts that allows to perform...
BioNetComp: a Python package for biological network development and comparison
BioNetComp compares two biologial networks from a list of genes/proteins. It provides both an easy-to-use...
dCCIforLAMMPS: dynamical Clausius-Clapeyron integration using LAMMPS
This repository contains a set of source codes and input scripts that allows to perform...
ChunkSplitters.jl: easy split the elements or indices of a collection into chunks.
https://juliafolds2.github.io/ChunkSplitters.jl/stable/#ChunkSplitters.jl ChunkSplitters.jl makes it easy to split the elements or indices of a collection into chunks:...
Cellulose-builder: a toolkit for building crystalline structures of cellulose
Cellulose-builder is a user-friendly program that builds crystalline structures of cellulose of different sizes and...
Packmol: A package to build initial configurations for molecular dynamics simulations
PACKMOL creates an initial point for molecular dynamics simulations by packing molecules in defined regions...
High Performance Collision Cross Section Calculation – HPCCS
High Performance Collision Cross Section Calculation – HPCCS The High Performance Collision Cross Section (HPCCS)...
IIS – Integrated Interactome System
A Web-Based Platform for the Annotation, Analysis and Visualization of Protein-Metabolite-Gene-Drug Interactions by Integrating a...
ComplexMixtures.jl: A package to study the structure of solutions formed by solutes and solvents of complex molecular shapes.
ComplexMixtures is a Julia package to study the solute and solvent interactions of mixtures of...
KernelFaRer: Replacing Native-Code Idioms with High-Performance Library Calls
N-body simulations and trajectory analysis rely on the calculation of attributes that depend on KernelFaRer...
FluidFreeEnergyforLAMMPS: Nonequilibrium Free-Energy Calculations of Fluids using LAMMPS
Scripts that allows to perform nonequilibrium free-energy calculations of fluid-phase systems using LAMMPS code. Details...