Helpful Online tools:
The Multiple Sequence Alignment tool: Clustal Omega for aligning three or more amino acid FASTA sequences. For two sequences, Pairwise Sequence Alignment.
System prepararion: CHARMM-GUI
3D protein/DNA/RNA/Structures: RCSB protein data bank
3D structure prediction: AlphaFold Colab
Protein-Protein, Protein-DNA/RNA, Protein-Ligand docking: HDOCK SERVER
Glycan reader and modeling.
For dabbling in data science: Kaggle
A Source of GROMACS tutorial.
Md analysis and modeling resource by CD ComputaBio.
Contact map calculation: Conan
Basic of MD simulation before starting: 1. Foundations in MD 2. MD of Lipid Membrane
Removing white background from a picture using IO Imageonline.co
Good source for basics of Molecular Dynamics Simulation: Amber Project
Adding colors for Xmgrace & more color options from the color brewer.
Free Biochemistry material from Kevin Ahern of OSU.
For Physics Job, please see here.
DeepTMHMM: A Transmembrane Topology Prediction and Classification
Structural alignment can be done here.
Sharing data for publication, Zenodo is an open and free repository operated by CERN.
A summer boot camp on scientific computing fhttps://pdb-redo.eu/dsspor beginners with Python and PyTorch organized by Pratyush Tiwary.
Protein secondary structure predictor: DSSP.
Reading about Tamás Hegedűs: https://hpc.kifu.hu/en/hegedus_tamas
Residue renumbering can be done using canoz
Pore formation and it's analysis with CHAP.
Protein Cluster analysis.
pH and pKa value calculation using poissonboltzmann[dot]org. (chosse- pH 7.0, chosse- Use PROPKA to assign protonation states at provided pH, finally check the pqr file to see the changes in HIS residues)
Bryce group link for Amber parameter database.
For covalent docking, GNINA developed by Prof. David Koes can be used.