- Why Cyscore has no term for charge-charge interaction
between protein and ligand?
Charge–charge interaction may play a critical role in some
of protein–ligand interaction. However, its net effect on bind-
ing affinity is very complicated and pH-dependent. Cyscore
ignores this term. - How do the programs do with HETATM records in PDB file?
Programs in Cyscore package ignore the HETATM records
in PDB file. If the head markers of “HETATM” are replaced by
“ATOM,” they will be taken into account. - Can I use other programs to add hydrogen atoms to the
protein?
Yes. Cyscore supports any protein file in standard PDB
format. - What is RotaBond used for?
RotaBond is used for estimating entropy loss of ligand in
binding process in Cyscore. In other cases, it is used in lead-like
compounds screening. For example, lead-like compounds fol-
low some experience-based rules, such as the rule of three
(RO3), which restricts the number of rotatable bonds. - Does Cyscore work on Windows system?
Current Cyscore package works on Linux. The Windows
version will be released in future.
Acknowledgments
We gratefully thank Dr. Shuang Chen for the help with critical
editing of the manuscript. The work was supported by the National
Natural Science Foundation of China (#31401130 to Y.C).References
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