3D-ConMap Protocol: Mapping Amino Acid Conservation onto 3D Protein Structures
Description
3D-ConMap is a tool for structural-functional analysis of amino acid sequence conservation, integrating multiple sequence alignment (MSA) data with 3D protein structures. It enables direct color-coding of conserved and variable residues on PDB models (ranges: 100–90%, 90–80%, 80–70%, 70–50%, 50–30%, 30–10%, <10%) derived from MSA analysis. The output script generates results functionally equivalent to ConSurf, while remaining independent of server availability or computational constraints.
Files
Steps to reproduce
Workflow 1. Homolog database creation using existing databases or custom datasets created with BLAST, PSI-BLAST, PHI-BLAST, or similar algorithms. 2. MSA construction from selected sequences using MAFFT, ClustalO, etc., using Jalview software. 3. Target structure extraction from PDB (www.rcsb.org), AlphaFold DB (alphafold.ebi.ac.uk), or AlphaFold server modeling (alphafoldserver.com). 4. Target sequence and MSA conservation extraction using Jalview software. 5. Conservation assignment of target sequence using Script EXT_Cons_for_3DMSA.txt, generating target protein conservation output. 6. Insert conservation data into 3D-ConMap_PyMOL_.pml. script and save changes. Rename target protein 3D model as Target_3DConMap.pdb. 7. Load target structure Target_3DConMap.pdb in PyMOL and run resulted 3D-ConMap_PyMOL_.pml script. 8. Optional: Apply color scheme—Standard (slate→violetpurple), ConSurf-like, or custom configuration (can be found in the file PyMOL_cmd_color gradients.txt) 9. Analyze conservation patterns within the target protein 3D model.