2. Overview of Protein and Structures

PDBe was utilized for presenting and visualizing protein structures. Additionally, PDBe facilitates a superposition view that overlays observed ligand molecules on representative protein conformations. To view the 3D structures, users can access the detailed information page.

3. The basic physicochemical properties

To derive the physical and chemical properties of proteins stored in MERITS, we rely on ProtParam. This tool enables computation of a suite of parameters, including molecular weight, theoretical p value, atomic composition, extinction coefficient, estimated half-life, instability index, aliphatic index, and grand average of hydropathicity. Results of ProtParam analyses can be viewed on the detailed information page.

4. The hydrophobicity information

Additionally, we utilize ProtScale to calculate and depict the amino acid scale profile on a specific protein.

5. Subcellular Location

Initially, subcellular localization was predicted using TBpred. Subsequently, signal peptides and transmembrane helices were identified using SignalP 6.0 and TMHMM 2.0. Finally, SecretomeP 2.0 was utilized to identify whether the protein is classified as non-classical secretory.

6. Protein histidine phosphorylation sites prediction

The PROSPECT tool was employed to analyze the histidine phosphorylation sites of proteins within MERITS. The predicted results were subsequently obtained and provided to users as a reference.

7. Protein function prediction

DeepGOPlus was utilized to predict protein functions, which included GO terms from the Biological Process, Molecular Function, and Cellular Component sub-ontologies, along with their respective confidence scores.

8. Antigenicity, Toxicity and Allergenicity prediction

VaxiJen, Toxinpred2 and AllerTOP were used to determine Antigenicity, Toxicity and Allergenicity of each protein in MERITS.

9. Protein fuction prediction

BLASTp was used to predict homology between PE/PPE proteins and H. sapiens proteins (ref: GRCh38.p14). And blasterJS was used to visualize the results.

10. Linear B-cell epitope prediction

We use ABCpred to predict B cell epitope(s) in PE/PPE proteins' sequence.

11. Secondary Structure of Protein

The NetSurfP - 3.0 Model predicts the surface accessibility, secondary structure, disorder, and phi/psi dihedral angles of amino acids in an amino acid sequence.

12. Timeline

The Timeline page contains all updates of the project and enables tracking of prior data versions.

Access to the Timeline page is also available through the links on the Home and Download pages.

13. Submit New Questions or New Proteins

The SUBMISSION page allows users to submit information about new proteins, with required fields marked by a red asterisk. Upon receiving the user's submission, we will commence the submission request and contact the user if necessary.