FAQs
For questions not addressed by a support solution here, please Contact Us. Please do include a description of the problem as well as your operating system and version.
What can we help you with?
-
Why are my H-bond constraints not being taken into account?
… should be a H-bond acceptor. The protein atom should be available for ligand binding (e.g. solvent accessible). You can see if the atoms involved in your H-bond …
-
How should I reference SuperStar?
… , 1999 [DOI: 10.1006/jmbi.1999.2809] SuperStar: Improved knowledge-based interaction fields for protein binding sites M. L. Verdonk, J. C. Cole, P. Watson, V. Gillet …
-
Can I perform a rigid ligand docking using GOLD?
… Although GOLD was designed to dock flexible ligands into protein binding sites, it is possible to perform a rigid ligand docking. To enable this option, go …
-
Has GOLD been validated?
… program can then be used to predict the binding mode of the ligand and a comparison made with the crystallographically observed position. Using this methodology …
-
How do I define my active site?
… containing a list of residues When using a list of residues to define the binding site the file must be in the following format: > HIS69 ARG71 GLU72 ARG127 ASN144 …
-
Does GOLD allow for protein flexibility?
… . The starting positions of Ser, Thr and Tyr OH groups and Lys NH3+ groups therefore do not matter. In cases where you are docking a ligand into a binding site …
-
Is it possible to include any additional probe groups?
… useful probes to start exploring a binding site are usually: Alcohol Oxygen: the hydroxyl group can both donate and accept hydrogen bonds, so favorable spots …
-
How can I calculate a score per binding site residue?
… How can I calculate a score per binding site residue? …
Top Support Solutions
- CSD Portfolio software suites requirements and supported platforms
- What is the difference between the GoldScore, ChemScore, ASP and ChemPLP scoring functions provided with GOLD?
- How does the GOLD licensing system work?
- How do I sign into WebCSD and what are the benefits of signing in?
- How should I reference GOLD?
Newest Support Solutions
- How do I ensure I get the best performance from CSD-CrossMiner?
- "Invalid window handle" error when using the CSD Python API on Windows
- Picking atoms in Mercury or Hermes stopped working after I upgraded to 2024.2
- Crystallisability and solvate prediction scripts not working in 2024.2 release
- What should I do if I experience an error during deposition that prevents me from adding checkCIF alert responses?