Templates

Databases and Repositories

  • Proteins (structure, function, interactions, etc.):
    • RCSB Protein Data Bank - protein structures (often a good starting point for atomistic molecular dynamics simulations)
    • Uniprot - protein sequence and function
    • BCL2DB - sequence, structural, and functional data for Bcl-2 and BH3 containing proteins (involved for example in mitochondrial apoptosis regulation)
    • STRING - Protein-protein interaction networks and functional enrichment analysis.
    • BindingDB - binding affinities for proteins and drug-like molecules
    • Human Protein Atlas - data on the human proteome.
    • SuPepMem - molecular dynamics simulations of peptides interacting with membranes, including input files, trajectories, and some analysis outputs.
    • IntAct - macromolecular interaction data
    • MD Repo - molecular dynamics simulations of proteins, with and without ligands.
  • Small molecules (drugs and other biologically relevant molecules):
  • Biological pathways:
  • Biological models:
    • BioModels - mathematical models of biological systems
  • Biological quantities:
    • Bionumbers - broad range of biological/molecular biology quantities
  • Cancer:
    • COSMIC - somatic mutations in cancer
  • Genomics:
    • KEGG - genes and genomes
    • PharmGKB - pharmacogenomics information
    • GEO - functional genomics data
    • OMIM - human genes and genetic disorders
    • ENCODE - functional genomics and characterization data

Software

  • molecular dynamics simulation, docking, molecular visualization, etc.:
    • LAMMPS - classical molecular dynamics simulator
    • GROMACS - classical molecular dynamics simulator and analysis
    • NAMD - classical molecular dynamics simulator targeted to biomolecular systems
    • VMD - molecular visualization and analysis
    • CHARMM-GUI - molecular dynamics simulation system construction and input generation.
    • CaFE - plugin for VMD providing an interface for MM/PBSA analysis to compute binding free energies
    • APBS - Adaptive Poisson-Boltzmann Solver for MM/PBSA calculations
    • MDAnalysis - Python library for molecular dynamics simulation analysis
    • MDTraj - Python library for molecular dynamics simulation analysis
    • Avogadro - Visualization, molecule editing, and simulation
    • PyMOL - Python library for molecular visualization
    • ngliew - Jupyter/IPython widget to render and view molecular structures inside notebooks.
    • KFC Server - protein-protein binding hotspot prediction
    • ClusPro - protein-protein docking
    • SWISS-MODEL - protein homology modeling
    • Rosetta - protein structure analysis, docking, homology modeling, and more.
  • biological pathway/reaction network/systems biology modeling:
    • PySB - rules-based reaction network model specification and simulation using the Python programming language (ODE or SDE models)
    • BioNetGen - rules-based reaction network model specification and simulation (ODE or SDE models)
    • SBML - reaction network model specification
    • Smoldyn - particle-based spatial stochastic simulation of diffusion and reaction networks.
    • NEURON - spatial reaction-diffusion simulations (PDE for diffusion plus ODE for reactions) - this package is geared towards developing computational models of neurons, but can be used more generally for reaction-diffusion simulations. It also has a nice extracellular space simulator that incorporates volume fraction and tortuosity. And it can be used as a Python library.
    • Catalyst.jl - reaction network model specification and generation using the Julia programming language (ODE, SDE, or jump models)
    • MCell - particle-based spatial stochastic simulation of diffusion and reaction networks.