Packmol: A package to build initial configurations for molecular dynamics simulationsLeandro MartinezDezembro 8, 2018Dezembro 10, 2018Dezembro 8, 2018Dezembro 10, 201805579PACKMOL creates an initial point for molecular dynamics simulations by packing molecules in defined regions...
Cellulose-builder: a toolkit for building crystalline structures of celluloseLeandro MartinezDezembro 9, 2018Abril 1, 2019Dezembro 9, 2018Abril 1, 201909975Cellulose-builder is a user-friendly program that builds crystalline structures of cellulose of different sizes and...
OmpCloud: Programming Cloud Clusters with OpenMPcces ccesNovembro 1, 2019Novembro 1, 2019Novembro 1, 2019Novembro 1, 201901560OmpCloud is a toolset that allows you to use the cloud as an OpenMP offloading...
DNN-ROM: a software to construct reduced order models and fluid flowscces ccesAbril 16, 2019Maio 2, 2019Abril 16, 2019Maio 2, 201903793...
dCCIforLAMMPS: dynamical Clausius-Clapeyron integration using LAMMPScces ccesOutubro 21, 2022Outubro 21, 2022Outubro 21, 2022Outubro 21, 20220830This repository contains a set of source codes and input scripts that allows to perform...
MDLovoFit: Automatic identification of mobile and rigid substructure in protein dynamicsLeandro MartinezDezembro 8, 2018Dezembro 10, 2018Dezembro 8, 2018Dezembro 10, 201802129MDLovoFit is a package for the analysis of the mobility and structural fluctuation in Molecular...
TMFree: A Compiler Mechanism to Elide Unnecessary Barriers in Transactional Memory Codecces ccesOutubro 21, 2022Outubro 21, 2022Outubro 21, 2022Outubro 21, 20220845TMFree is a compiler mechanism implemented in LLVM that allows programmers to precisely identify and...
MassCCS: Massive Collision Cross Section calculations for large macromolecular assembliescces ccesMaio 29, 2023Maio 29, 2023Maio 29, 2023Maio 29, 202301124This repository contains a set of source codes and input scripts that allows to perform...
BioNetComp: a Python package for biological network development and comparisoncces ccesMaio 31, 2021Maio 31, 202103514BioNetComp compares two biologial networks from a list of genes/proteins. It provides both an easy-to-use...
ComplexMixtures.jl: A package to study the structure of solutions formed by solutes and solvents of complex molecular shapes.cces ccesMaio 31, 2021Maio 31, 2021Maio 31, 2021Maio 31, 202102176ComplexMixtures is a Julia package to study the solute and solvent interactions of mixtures of...
PeNTIOS: a package for Petri Net simulation in Saccharomyces cerevisiaecces ccesAbril 4, 2019Abril 8, 2019Abril 4, 2019Abril 8, 201901464...
IIS – Integrated Interactome Systemcces ccesAbril 4, 2019Abril 8, 2019Abril 4, 2019Abril 8, 201902014A Web-Based Platform for the Annotation, Analysis and Visualization of Protein-Metabolite-Gene-Drug Interactions by Integrating a...
CellListMap.jl: Efficient and customizable cell list implementation for calculation of pairwise particle properties within a cutoffcces ccesJunho 23, 2022Outubro 21, 2022Junho 23, 2022Outubro 21, 20220928L. Martínez, CellListMap.jl: Efficient and customizable cell list implementation for calculation of pairwise particle properties...
LovoAlign: General molecular structural alignment packageLeandro MartinezDezembro 8, 2018Dezembro 10, 2018Dezembro 8, 2018Dezembro 10, 201802165LovoAlign is a new protein structural alignment package. The methods used for structural alignment are...
KernelFaRer: Replacing Native-Code Idioms with High-Performance Library Callscces ccesOutubro 21, 2022Outubro 21, 2022Outubro 21, 2022Outubro 21, 20220855N-body simulations and trajectory analysis rely on the calculation of attributes that depend on KernelFaRer...
High Performance Collision Cross Section Calculation – HPCCSLeandro MartinezDezembro 9, 2018Dezembro 10, 2018Dezembro 9, 2018Dezembro 10, 201802449High Performance Collision Cross Section Calculation – HPCCS The High Performance Collision Cross Section (HPCCS)...
ChunkSplitters.jl: easy split the elements or indices of a collection into chunks.cces ccesJunho 11, 2025Junho 11, 2025Junho 11, 2025Junho 11, 2025041https://juliafolds2.github.io/ChunkSplitters.jl/stable/#ChunkSplitters.jl ChunkSplitters.jl makes it easy to split the elements or indices of a collection into chunks:...
FluidFreeEnergyforLAMMPS: Nonequilibrium Free-Energy Calculations of Fluids using LAMMPScces ccesMaio 31, 2021Maio 31, 2021Maio 31, 2021Maio 31, 202103606Scripts that allows to perform nonequilibrium free-energy calculations of fluid-phase systems using LAMMPS code. Details...
TopoLink: A package to evaluate structural models using chemical crosslinking distance constraints.Leandro MartinezDezembro 8, 2018Dezembro 10, 2018Dezembro 8, 2018Dezembro 10, 201801964TOPOLINK is a package to compute topological distances between atoms on the surface of proteins...
PGA: a Polyploid Gene Assemblercces ccesAbril 4, 2019Janeiro 28, 2020Abril 4, 2019Janeiro 28, 202002882PGA was developed using PERL scripts for running in Linux system and integrates various software...