Blog

Learn how to prepare a protein and ligand for docking, clean the PDB, add hydrogens and charges, and export PDBQT files. Get docking-ready today.

15 free computational biology project ideas (docking + MD) for MSc and final-year students. See what each proves to a PI and start building your CV today.

Compare the best free molecular docking software for students in 2026 (AutoDock Vina, SwissDock, DiffDock). See costs, GPU needs and where to start.

Compare GROMACS, AMBER, NAMD, OpenMM and LAMMPS on license, GPU, and beginner-friendliness. See the best free MD engine for students and start learning.

Docking predicts where a molecule binds; molecular dynamics simulates how the complex moves. Key differences, when to use each, and which to learn first.

A clear beginner’s guide to density functional theory (DFT), how it predicts material and molecular properties from electron density, and how to start.

A beginner’s guide to molecular docking: what it is, how it predicts protein-ligand binding, why it matters for drug discovery, and how to get started.

Learn what sequence alignment is, how pairwise and multiple alignment work, how scoring and gaps are handled, and the beginner tools used in real research.

A beginner’s guide to finite element analysis (FEA): what it is, how meshing and the math work, the workflow, and the tools used in real projects.

Learn about protein binding sites, their types (active, allosteric), and how computational tools identify them for drug design and molecular modeling.