Helpful Online tools:

1. The Multiple Sequence Alignment tool: Clustal Omega for aligning three or more amino acid FASTA sequences. For two sequences, Pairwise Sequence Alignment.

2. System prepararion: CHARMM-GUI

3. 3D protein/DNA/RNA/Structures: RCSB protein data bank 

4. 3D structure prediction: AlphaFold Colab

5. Protein-Protein, Protein-DNA/RNA, Protein-Ligand docking: HDOCK SERVER

6. Glycan reader and modeling.

7. For dabbling in data science: Kaggle

8. A Source of GROMACS tutorial.

9. Md analysis and modeling resource by CD ComputaBio.

10. Contact map calculation: Conan

11. Basic of MD simulation before starting: 1. Foundations in MD 2. MD of Lipid Membrane

12. Removing white background from a picture using IO Imageonline.co

13. Good source for basics of Molecular Dynamics Simulation: Amber Project

14. Adding colors for Xmgrace & more color options from the color brewer.

15. Protein Structure Analysis.

16. Free Biochemistry material from Kevin Ahern of OSU.

17. For Physics Job, please see here.

18. DeepTMHMM: A Transmembrane Topology Prediction and Classification

19. Structural alignment can be done here.

20. Sharing data for publication, Zenodo is an open and free repository operated by CERN.

21. A summer boot camp on scientific computing fhttps://pdb-redo.eu/dsspor beginners with Python and PyTorch organized by Pratyush Tiwary.

22. Protein secondary structure predictor: DSSP.

23. Reading about Tamás Hegedűs: https://hpc.kifu.hu/en/hegedus_tamas