PGA: a Polyploid Gene Assemblercces ccesAbril 4, 2019Janeiro 28, 2020Abril 4, 2019Janeiro 28, 202012329PGA was developed using PERL scripts for running in Linux system and integrates various software...
Cellulose-builder: a toolkit for building crystalline structures of celluloseLeandro MartinezDezembro 9, 2018Abril 1, 2019Dezembro 9, 2018Abril 1, 201907813Cellulose-builder is a user-friendly program that builds crystalline structures of cellulose of different sizes and...
High Performance Collision Cross Section Calculation – HPCCSLeandro MartinezDezembro 9, 2018Dezembro 10, 2018Dezembro 9, 2018Dezembro 10, 201801862High Performance Collision Cross Section Calculation – HPCCS The High Performance Collision Cross Section (HPCCS)...
MassCCS: Massive Collision Cross Section calculations for large macromolecular assembliescces ccesMaio 29, 2023Maio 29, 2023Maio 29, 2023Maio 29, 20230474This repository contains a set of source codes and input scripts that allows to perform...
dCCIforLAMMPS: dynamical Clausius-Clapeyron integration using LAMMPScces ccesOutubro 21, 2022Outubro 21, 2022Outubro 21, 2022Outubro 21, 20220357This 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, 202103002BioNetComp compares two biologial networks from a list of genes/proteins. It provides both an easy-to-use...
OmpCloud: Programming Cloud Clusters with OpenMPcces ccesNovembro 1, 2019Novembro 1, 2019Novembro 1, 2019Novembro 1, 201901149OmpCloud is a toolset that allows you to use the cloud as an OpenMP offloading...
LovoAlign: General molecular structural alignment packageLeandro MartinezDezembro 8, 2018Dezembro 10, 2018Dezembro 8, 2018Dezembro 10, 201801663LovoAlign is a new protein structural alignment package. The methods used for structural alignment are...
PeNTIOS: a package for Petri Net simulation in Saccharomyces cerevisiaecces ccesAbril 4, 2019Abril 8, 2019Abril 4, 2019Abril 8, 201901121...
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, 202101548ComplexMixtures is a Julia package to study the solute and solvent interactions of mixtures of...
IIS – Integrated Interactome Systemcces ccesAbril 4, 2019Abril 8, 2019Abril 4, 2019Abril 8, 201901520A Web-Based Platform for the Annotation, Analysis and Visualization of Protein-Metabolite-Gene-Drug Interactions by Integrating a...
MDLovoFit: Automatic identification of mobile and rigid substructure in protein dynamicsLeandro MartinezDezembro 8, 2018Dezembro 10, 2018Dezembro 8, 2018Dezembro 10, 201801438MDLovoFit is a package for the analysis of the mobility and structural fluctuation in Molecular...
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, 20220467L. Martínez, CellListMap.jl: Efficient and customizable cell list implementation for calculation of pairwise particle properties...
TMFree: A Compiler Mechanism to Elide Unnecessary Barriers in Transactional Memory Codecces ccesOutubro 21, 2022Outubro 21, 2022Outubro 21, 2022Outubro 21, 20220393TMFree is a compiler mechanism implemented in LLVM that allows programmers to precisely identify and...
KernelFaRer: Replacing Native-Code Idioms with High-Performance Library Callscces ccesOutubro 21, 2022Outubro 21, 2022Outubro 21, 2022Outubro 21, 20220350N-body simulations and trajectory analysis rely on the calculation of attributes that depend on KernelFaRer...
Packmol: A package to build initial configurations for molecular dynamics simulationsLeandro MartinezDezembro 8, 2018Dezembro 10, 2018Dezembro 8, 2018Dezembro 10, 201803679PACKMOL creates an initial point for molecular dynamics simulations by packing molecules in defined regions...
FluidFreeEnergyforLAMMPS: Nonequilibrium Free-Energy Calculations of Fluids using LAMMPScces ccesMaio 31, 2021Maio 31, 2021Maio 31, 2021Maio 31, 202103056Scripts 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, 201801452TOPOLINK 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, 201903013...