softwares.md

Alinhamento de sequências

Jalview (https://www.jalview.org/)

MEGA (https://www.megasoftware.net)

BLAST (https://blast.ncbi.nlm.nih.gov/Blast.cgi)

MUMmer (https://github.com/mummer4/mummer)

Clustal Omega (https://www.ebi.ac.uk/Tools/msa/clustalo/)

MAFFT (https://mafft.cbrc.jp/alignment/software/)

MUSCLE (https://www.ebi.ac.uk/Tools/msa/muscle/)

T-COFFEE (https://tcoffee.crg.eu/)

Modelagem molecular

SWISS-MODEL (https://swissmodel.expasy.org/)

MODELLER (https://salilab.org)

AlphaFol2 (https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb)

Docking Molecular

Autodock Vina (https://vina.scripps.edu/)

DOCK6 (https://dock.compbio.ucsf.edu/DOCK_6/index.htm)

Autodock4 (https://autodock.scripps.edu/)

MGLTools (https://ccsb.scripps.edu/mgltools/)

HPEPDOCK Server (http://huanglab.phys.hust.edu.cn/hpepdock/)

Dinâmica molecular

Gromacs (https://www.gromacs.org/)

Amber (https://ambermd.org/)

Visualização

Pymol (https://pymol.org/2/)

Chimera (https://www.cgl.ucsf.edu/chimera/download.html)

Discovery Studio (https://www.3ds.com/products-services/biovia/products/molecular-modeling-simulation/biovia-discovery-studio/)

Avogadro (https://avogadro.cc/)

Descritores químicos (QSAR)

Chemistry Development Kit (https://cdk.github.io/)

RDKit (https://www.rdkit.org/)

Open Babel (http://openbabel.org/wiki/Main_Page)

Padel-Descriptor (http://www.yapcwsoft.com/dd/padeldescriptor/)

Pydel (https://github.com/rolsdorph/pydel)

Programação

Python (https://www.python.org/)

Anaconda Python (https://www.anaconda.com/products/distribution)

Biopython (https://biopython.org)

Shell Script (https://pt.wikipedia.org/wiki/Shell_script)

BioPerl (https://bioperl.org)

Biojava (https://biojava.org)

Scikit-Bio (http://scikit-bio.org/docs/0.1.3/index.html)

Ferramentas de bioinformática

Galaxy (https://usegalaxy.org/)

Emboss (https://www.bioinformatics.nl/emboss-explorer/)

BioPep (https://github.com/lucaspalmeira/BioPep)

Fóruns

BioStars (https://www.biostars.org/)

Pt StackOverFlow (https://pt.stackoverflow.com/)

Viva o Linux (https://www.vivaolinux.com.br/)

Ask Ubuntu (https://askubuntu.com/)

Cursos

Introdução à Ciência da Computação com Python Parte 1 (https://pt.coursera.org/learn/ciencia-computacao-python-conceitos)

Introdução a Ciência de Dados (https://www.datascienceacademy.com.br/cursosgratuitos)

Bases de dados

GenBank (https://www.ncbi.nlm.nih.gov/genbank/)

Protein Data Bank - PDB (https://www.rcsb.org)

Pubchem (https://pubchem.ncbi.nlm.nih.gov)

Drug Bank (https://go.drugbank.com/)

Zinc 15 (https://zinc15.docking.org/)

ChEMBL (https://www.ebi.ac.uk/chembl/)

Swissprot (https://www.expasy.org/resources/uniprotkb-swiss-prot)

Uniprot (https://www.uniprot.org/)

ChEBI (https://www.ebi.ac.uk/chebi/)

APD3 - Antimicrobial Peptide Database (https://aps.unmc.edu/)

PepBDB (http://huanglab.phys.hust.edu.cn/pepbdb/)