Question: What is a .pqr file?
Answer:
A .pqr file is an ascii text file containing position-coordinates (p),
partial atomic charges (q), and atom size (r) for atoms in the molecule.
Question: Does BION-2 accept .pqr files with missing hydrogen?
Answer: NO. Hydrogen atoms must be present.
Question: What about missing residues?
Answer:
Missing residues must be modeled before generating .pqr.
Question: Can atom sizes be zero?
Answer: NO. Zero atom size is unphysical.
Question: Small molecules bound to protein?
Answer:
Supported, as long as p, q, r values exist in the .pqr file.
Question: Can all charges be zero?
Answer: NO. Charge information is required.
Question: Why .pqr instead of .pdb?
Answer:
.pqr allows incorporating protonation state and pH effects.
Question: How to generate .pqr?
Answer:
Use tools like
DelphiPka,
pdb2pqr, or Reduce.
Question: How should I cite results from this server?
Answer:
Please cite the references most relevant to what you used. For most users, the primary citation is the
BION-2 server paper.
Primary citation: BION-2
Shashikala HBM, Chakravorty A, Panday SK, Alexov E. BION-2: Predicting Positions of Non-Specifically Bound Ions on Protein Surface by a Gaussian-Based Treatment of Electrostatics.
International Journal of Molecular Sciences. 2021; 22(1):272.
doi:10.3390/ijms22010272.
DelPhi method and software
Li C., Jia Z., Chakravorty A., Pahari S., Peng Y., Basu S., Koirala M.,
Panday S.K., Petukh M., Li L., Alexov E. DelPhi Suite: New Developments
and Review of Functionalities. Journal of Computational Chemistry.
2019;40(28):2502–2508. doi:10.1002/jcc.26006.
Interactive visualization
Rego N., Koes D. 3Dmol.js: molecular visualization with WebGL.
Bioinformatics. 2015;31(8):1322–1324.
doi:10.1093/bioinformatics/btu829.
You do not need to cite every reference above for every use case. Cite BION-2 for calculations from this server,
add DelPhi references when those are relevant to your discussion, and cite 3Dmol.js only when
you use visualization generated through the server.
