Table 1.
List of servers used in the computational analysis:
Si No: | Name of web server | Function | Reference | Submission parameters |
---|---|---|---|---|
1 | mCSM | Predict protein stability changes due to mutations. | [28] | Model PDB file, mutation and chain id. |
2 | SDM | Predict protein stability changes due to mutations. | [18] | Model PDB file, mutation and chain id. |
3 | mCSM-PPI | Predict stability of protein–protein interfaces due to mutations. | [28] | Model PDB file, mutation and chain id. |
4 | mCSM-NA2 | Predict stability of protein-nucleic acid interactions due to mutations | [29] | Model PDB file, mutation, chain id and nucleic acid type. |
5 | mCSM-lig | Stability of protein–ligand interactions due to mutations | [30] | Model PDB file, mutation, chain id, three letter code of the ligand and ligand affinity in wild type structure in nM concentration. |
6 | FoldX4 | Predict protein stability changes due to mutations. | [19] | Model PDB file, list of mutations and chain ids. |
7 | MAESTRO | Predict protein stability changes due to mutations. | [31] | Model PDB file, list of mutations and chain ids. |
8 | CUPSAT | Predict protein stability changes due to mutations. | [32] | Model PDB file, list of mutations and chain ids. |
9 | Imutant 2.0-Struc | Predict protein stability changes due to mutations. | [33] | Model PDB file, list of mutations and chain ids. |
10 | Imutant 2.0 -Seq | Predict protein stability changes due to mutations using sequence information. | [33] | RNAP sequence file in fasta format, list of mutations and chain ids. |
11 | PROVEAN | Predict protein stability changes due to mutations using sequence information. | [34] | RNAP sequence file in fasta format, list of mutations and chain ids. |
12 | CONSURF | To calculate evolutionary conservation score of each residue in the protein. | [35] | Model PDB file |
13 | ENCoM | Conformational Changes in protein due to mutations. | [20] | Model PDB file, list of mutations and chain ids. |
14 | DynaMut | Conformational Changes in protein due to mutations. | [21] | Model PDB file, list of mutations and chain ids. |
15 | Arpeggio | Map interatomic interactions between wildtype and mutant amino acids and the residue environment. | [36] | Model PDB file and the residue selection in standard format. |
16 | Intermezzo | Map interatomic interactions between wildtype and mutant amino acids and the residue environment. | Bernardo Ochoa Montano & Blundell TL unpublished | Model PDB file and the residue selection in standard format. |
17 | ANDANTE | Works along with Modeller to generate mutant models from wildtype model files. | [26] | Model PDB file, mutation and chain id |
18 | Fragment Hotspot Maps | Maps regions on the surface of the protein that has high propensity for small molecule binding. | [22] | Model PDB file. |