Pinned Repositories
2021-04-22-qmmm-gromacs-cp2k
Repository for April 2021 training course in QM/MM simulation with GROMACS+CP2K
biobb
Biobb (BioExcel building blocks) packages are Python building blocks that create new layer of compatibility and interoperability over popular bioinformatics tools.
biobb_amber
Biobb_amber is a BioBB category for AMBER MD package.
biobb_md
Biobb_md is the Biobb module collection to perform molecular dynamics simulations.
biobb_structure_checking
CP2K_qmmm_input_preparation_scripts
A compilation of useful python scripts to create QM/MM CP2K inputfiles
cp2K_qmmm_tutorials_for_biological_simulations
Several QM/MM tutorials for biological simulations adapted to CP2K. Tutorials adapted from AMBER, GMX, NAMD and CPMD softwares.
gromacs-2022-cp2k-tutorial
Sample inputs and tutorial for GROMACS-2022/CP2K QMMM interface
gromacs-docker
Dockerfile for GROMACS
pymdsetup
BioExcel's Repositories
bioexcel/biobb_structure_checking
bioexcel/biobb_amber
Biobb_amber is a BioBB category for AMBER MD package.
bioexcel/biobb_md
Biobb_md is the Biobb module collection to perform molecular dynamics simulations.
bioexcel/biobb_chemistry
Biobb_chemistry is the Biobb module collection to perform chemistry over molecular dynamics simulations.
bioexcel/biobb_gromacs
bioexcel/biobb_analysis
Biobb_analysis is the Biobb module collection to perform analysis of molecular dynamics simulations.
bioexcel/biobb_workflows
Global repository for all the BioExcel Building Blocks Workflows
bioexcel/biobb_io
Biobb_io is the Biobb module collection to fetch data to be consumed by the rest of the Biobb building blocks.
bioexcel/biobb_pmx
Biobb_pmx is the Biobb module collection to perform PMX (http://pmx.mpibpc.mpg.de) executions.
bioexcel/biobb_structure_utils
Biobb_structure_utils is the Biobb module collection to modify or extract information from a PDB structure file, such as pulling out a particular model or chain, removing water molecules or ligands, or renumbering or sorting atoms or residues.
bioexcel/biobb_template
Biobb_template is a complete code template to promote and facilitate the creation of new Biobbs by the community.
bioexcel/biobb_cp2k
bioexcel/biobb_flexdyn
biobb_flexdyn is a BioBB category for studies on the conformational landscape of native proteins.
bioexcel/biobb_flexserv
Biobb_flexserv is a BioBB category for biomolecular flexibility studies on protein 3D structures.
bioexcel/biobb_ml
Biobb_ml is the Biobb module collection to perform machine learning predictions.
bioexcel/biobb_model
Biobb_model is the Biobb module collection to check and model 3d structures, create mutations or reconstruct missing atoms.
bioexcel/biobb_pytorch
Biobb_pytorch is the Biobb module collection to create and train ML & DL models using the popular PyTorch Python library.
bioexcel/biobb_remote
bioexcel/biobb_vs
Biobb_vs is the Biobb module collection to perform virtual screening studies.
bioexcel/biobb_wf_pmx_tutorial
This tutorial aims to illustrate how to compute a fast-growth mutation free energy calculation, step by step, using the BioExcel Building Blocks library (biobb).
bioexcel/biobb_dna
Biobb_dna is the Biobb module collection to perform analyses and transformations on nucleic acid trajectories and helical parameter data.
bioexcel/biobb_adapters
Biobb_adapters is the Biobb module collection to use the building blocks with several workflow managers.
bioexcel/biobb_cmip
bioexcel/biobb_common
Biobb_common is the base package required to use the biobb packages.
bioexcel/biobb_community_wfs
Repository for all the community BioExcel Building Blocks Workflows
bioexcel/biobb_documentation
Documentation for the creation of a new BioExcel building block from scratch.
bioexcel/biobb_haddock
biobb_haddock is the Biobb module collection to compute information-driven flexible protein-protein docking.
bioexcel/biobb_pdb_tools
bioexcel/galaxy-tools-compchem
:mega: Galaxy Tools for Computational Chemistry
bioexcel/utils_biobb