BioNetComp: a Python package for biological network development and comparisoncces ccesMaio 31, 2021Maio 31, 202103029BioNetComp compares two biologial networks from a list of genes/proteins. It provides both an easy-to-use...
LovoAlign: General molecular structural alignment packageLeandro MartinezDezembro 8, 2018Dezembro 10, 2018Dezembro 8, 2018Dezembro 10, 201801686LovoAlign is a new protein structural alignment package. The methods used for structural alignment are...
OmpCloud: Programming Cloud Clusters with OpenMPcces ccesNovembro 1, 2019Novembro 1, 2019Novembro 1, 2019Novembro 1, 201901181OmpCloud is a toolset that allows you to use the cloud as an OpenMP offloading...
MassCCS: Massive Collision Cross Section calculations for large macromolecular assembliescces ccesMaio 29, 2023Maio 29, 2023Maio 29, 2023Maio 29, 20230510This repository contains a set of source codes and input scripts that allows to perform...
PeNTIOS: a package for Petri Net simulation in Saccharomyces cerevisiaecces ccesAbril 4, 2019Abril 8, 2019Abril 4, 2019Abril 8, 201901151...
TopoLink: A package to evaluate structural models using chemical crosslinking distance constraints.Leandro MartinezDezembro 8, 2018Dezembro 10, 2018Dezembro 8, 2018Dezembro 10, 201801496TOPOLINK is a package to compute topological distances between atoms on the surface of proteins...
DNN-ROM: a software to construct reduced order models and fluid flowscces ccesAbril 16, 2019Maio 2, 2019Abril 16, 2019Maio 2, 201903062...
IIS – Integrated Interactome Systemcces ccesAbril 4, 2019Abril 8, 2019Abril 4, 2019Abril 8, 201901555A Web-Based Platform for the Annotation, Analysis and Visualization of Protein-Metabolite-Gene-Drug Interactions by Integrating a...
TMFree: A Compiler Mechanism to Elide Unnecessary Barriers in Transactional Memory Codecces ccesOutubro 21, 2022Outubro 21, 2022Outubro 21, 2022Outubro 21, 20220440TMFree is a compiler mechanism implemented in LLVM that allows programmers to precisely identify and...
dCCIforLAMMPS: dynamical Clausius-Clapeyron integration using LAMMPScces ccesOutubro 21, 2022Outubro 21, 2022Outubro 21, 2022Outubro 21, 20220387This repository contains a set of source codes and input scripts that allows to perform...
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, 20220508L. Martínez, CellListMap.jl: Efficient and customizable cell list implementation for calculation of pairwise particle properties...
FluidFreeEnergyforLAMMPS: Nonequilibrium Free-Energy Calculations of Fluids using LAMMPScces ccesMaio 31, 2021Maio 31, 2021Maio 31, 2021Maio 31, 202103101Scripts that allows to perform nonequilibrium free-energy calculations of fluid-phase systems using LAMMPS code. Details...
MDLovoFit: Automatic identification of mobile and rigid substructure in protein dynamicsLeandro MartinezDezembro 8, 2018Dezembro 10, 2018Dezembro 8, 2018Dezembro 10, 20183 1573MDLovoFit is a package for the analysis of the mobility and structural fluctuation in Molecular...
PGA: a Polyploid Gene Assemblercces ccesAbril 4, 2019Janeiro 28, 2020Abril 4, 2019Janeiro 28, 202012366PGA was developed using PERL scripts for running in Linux system and integrates various software...
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, 202101602ComplexMixtures is a Julia package to study the solute and solvent interactions of mixtures of...
KernelFaRer: Replacing Native-Code Idioms with High-Performance Library Callscces ccesOutubro 21, 2022Outubro 21, 2022Outubro 21, 2022Outubro 21, 20220389N-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, 201801914High Performance Collision Cross Section Calculation – HPCCS The High Performance Collision Cross Section (HPCCS)...
Packmol: A package to build initial configurations for molecular dynamics simulationsLeandro MartinezDezembro 8, 2018Dezembro 10, 2018Dezembro 8, 2018Dezembro 10, 201803777PACKMOL 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, 201908036Cellulose-builder is a user-friendly program that builds crystalline structures of cellulose of different sizes and...