Software – CCES Unicamp

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:...

LovoAlign: General molecular structural alignment package

Leandro MartinezDezembro 8, 2018Dezembro 10, 2018

Dezembro 8, 2018Dezembro 10, 201802662

LovoAlign is a new protein structural alignment package. The methods used for structural alignment are...

DNN-ROM: a software to construct reduced order models and fluid flows

cces ccesAbril 16, 2019Maio 2, 2019

Abril 16, 2019Maio 2, 201904363

...

TopoLink: A package to evaluate structural models using chemical crosslinking distance constraints.

Leandro MartinezDezembro 8, 2018Dezembro 10, 2018

Dezembro 8, 2018Dezembro 10, 201802433

TOPOLINK is a package to compute topological distances between atoms on the surface of proteins...

KernelFaRer: Replacing Native-Code Idioms with High-Performance Library Calls

cces ccesOutubro 21, 2022Outubro 21, 2022

Outubro 21, 2022Outubro 21, 202201307

N-body simulations and trajectory analysis rely on the calculation of attributes that depend on KernelFaRer...

TMFree: A Compiler Mechanism to Elide Unnecessary Barriers in Transactional Memory Code

cces ccesOutubro 21, 2022Outubro 21, 2022

Outubro 21, 2022Outubro 21, 202201283

TMFree is a compiler mechanism implemented in LLVM that allows programmers to precisely identify and...

BioNetComp: a Python package for biological network development and comparison

cces ccesMaio 31, 2021

Maio 31, 202104077

BioNetComp compares two biologial networks from a list of genes/proteins. It provides both an easy-to-use...

PGA: a Polyploid Gene Assembler

cces ccesAbril 4, 2019Janeiro 28, 2020

Abril 4, 2019Janeiro 28, 202003333

PGA was developed using PERL scripts for running in Linux system and integrates various software...

MDLovoFit: Automatic identification of mobile and rigid substructure in protein dynamics

Leandro MartinezDezembro 8, 2018Dezembro 10, 2018

Dezembro 8, 2018Dezembro 10, 201802961

MDLovoFit is a package for the analysis of the mobility and structural fluctuation in Molecular...

ComplexMixtures.jl: A package to study the structure of solutions formed by solutes and solvents of complex molecular shapes.

cces ccesMaio 31, 2021Maio 31, 2021

Maio 31, 2021Maio 31, 202102718

ComplexMixtures is a Julia package to study the solute and solvent interactions of mixtures of...

IIS – Integrated Interactome System

cces ccesAbril 4, 2019Abril 8, 2019

Abril 4, 2019Abril 8, 201902446

A Web-Based Platform for the Annotation, Analysis and Visualization of Protein-Metabolite-Gene-Drug Interactions by Integrating a...

High Performance Collision Cross Section Calculation – HPCCS

Leandro MartinezDezembro 9, 2018Dezembro 10, 2018

Dezembro 9, 2018Dezembro 10, 201802916

High Performance Collision Cross Section Calculation – HPCCS The High Performance Collision Cross Section (HPCCS)...

dCCIforLAMMPS: dynamical Clausius-Clapeyron integration using LAMMPS

cces ccesOutubro 21, 2022Outubro 21, 2022

Outubro 21, 2022Outubro 21, 202201360

This repository contains a set of source codes and input scripts that allows to perform...

Cellulose-builder: a toolkit for building crystalline structures of cellulose

Leandro MartinezDezembro 9, 2018Abril 1, 2019

Dezembro 9, 2018Abril 1, 2019010830

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

Leandro MartinezDezembro 8, 2018Dezembro 10, 2018

Dezembro 8, 2018Dezembro 10, 201806405

PACKMOL creates an initial point for molecular dynamics simulations by packing molecules in defined regions...

FluidFreeEnergyforLAMMPS: Nonequilibrium Free-Energy Calculations of Fluids using LAMMPS

cces ccesMaio 31, 2021Maio 31, 2021

Maio 31, 2021Maio 31, 202104138

Scripts that allows to perform nonequilibrium free-energy calculations of fluid-phase systems using LAMMPS code. Details...

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