Frequently Asked Questions
- What is ScoreL?
- What is the main difference between ScoreL and other docking software?
- Where is ScoreL located and how do I access it?
- How is ScoreL licensed?
- Where can I get further help?
- Has ScoreL been validated?
- Which platforms are supported?
- Can I run the program in parallel?
- Which file formats are supported?
- Does ScoreL allow for protein flexibility?
- Can ScoreL handle metals?
- Does ScoreL calculate atomic charges?
- What is the naming convention for ligand output files?
- Is it possible to re-score a given set of ScoreL solutions using an alternative scoring function?
ScoreL is a new original tool for docking, scoring and virtual screening. It is designed to predict how small molecules, ligands, bind to a protein active site of known 3D structure.
2. What is the main difference between ScoreL and other docking software?
The fundamental difference of ScoreL from similar software is that ScoreL does not suggest a universal solution for any problem in structure-based drug design. ScoreL is merely a tool you need to adjust to your specific problem to solve it. ScoreL helps you to mine correctly as much information from available experimental data as possible. The more experiments, the more experience. For these purposes ScoreL suggests the user a set of original methods such as: target function for docking development, active ligand based scoring function development, inactive ligand based virtual screening post-processing and et al. For further information, please see www.didiall.com/products/.
3. Where is ScoreL located and how do I access it?
ScoreL 1.0 is a free demo version of ScoreL 1.1. ScoreL 1.0 is available at www.didiall.com/downloads/. ScoreL 1.0 is a totally free of charge. ScoreL 1.1 is commercial software and if you want to obtain it, please contact info@didiall.com.
ScoreL 1.0 is a free demo version of ScoreL 1.1. ScoreL 1.0 is a totally free of charge. ScoreL 1.1 is commercial software and if you want to obtain it, please contact info@didiall.com.
5. Where can I get further help?
Documentation for ScoreL 1.0 is available in the form of the User's Manual at the official ScoreL website (www.didiall.com/support/documentation.html) in HTML and PDF forms. If you need more help or information, please contact us: support@didiall.com.
Each ScoreL method has been validated. Validation results are available at www.didiall.com/products/.
7. Which platforms are supported?
ScoreL 1.0 and ScoreL 1.1 are supported on the following platforms and operating systems:
- Windows - Intel compatible, 32 bit, Windows 2000, XP and Vista
- Linux - Intel compatible, 32 & 64 bit: RedHat Enterprise 3.0, 4.0 and 5.0.
You need also PC with:
- Processor: Intel P4 or higher, AMD Athlon 64 or higher
- Memory: 1 GB RAM or more
- Free Disk Space: 100 MB or more
- Software: openGL
8. Can I run the program in parallel?
ScoreL 1.0 is a serial program and can not be run in parallel. ScoreL 1.1 can be run in parallel and distribute jobs over the network across a virtual cluster of machines in order to harness the processing power of multiple machines (or mutliple processors or processor cores) concurrently.
9. Which file formats are supported?
Acceptable ligand file formats are mol2 (i.e. Tripos format, http://www.tripos.com/data/support/mol2.pdf) or sdf (i.e. MDL Isis SDF file format, http://www.mdl.com/downloads/public/ctfile/ctfile.jsp). Files in sdf format may also have the extension .mdl or .mol. You may only use the extension .sdf. Acceptable protein file formats are pdb (wwPDB (v.2.3), http://www.wwpdb.org/documentation/).
10. Does ScoreL allow for protein flexibility?
During one docking or screening procedure protein that is used for binding site is considered to be rigid, it does not change during docking. In practice, many proteins are rather flexible. To consider protein flexibility in ScoreL, use several conformations of one protein, i.e. possible variants of protein changing during binding with ligand. Execute docking of one ligand to all protein conformations and integrate docking results using tab "integrate results". For further information, please refer to the ScoreL documentation.
Program ScoreL considers ligands interaction with metal ions in protein binding site. Metal ions could be ions of Ca, Fe, Co, Cd, Mg, Mn, Zn, Ga.
12. Does ScoreL calculate atomic charges?
ScoreL ignores both formal and partial charges. In the case of protonation mode in docking task is set up in "from structure" ScoreL deduces whether an atom is charged by counting the bond order of the atom and comparing the result with the atom's normal valency. In the case of protonation mode in docking task is set up in "auto" ScoreL calculates ionized states itself. For this reason, it is essential that the bond and atom types are set up correctly for both the protein and the ligand. For further information, please refer to the ScoreL documentation.
13. What is the naming convention for ligand output files?
Docking/screening results are saved in directory specified as "directory for results". Each ligand will have file where all best positions shall be stored. The following scheme is used to create name of resulting file: name = name of initial ligand file_(number of ligand in initial file)_name of ligand. For example, if initial structure of ligand was in file "ligand.mol2" and ligand with name "substance" was second in this file, then resulting file name for that ligand will be "ligand_2_substance.mol2".
Yes, it is possible. To obtain more correct results you need to local minimize ScoreL ligand positions using you own scoring function. ScoreL dose not provide you with the option of including your own scoring function in it. That is why you need to make it yourself.