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MODE
Receptor File
Ligand File
SEPARATE_MIN_DEPTH
MAX_ABSTRACT_LIMIT
SEPARATE_MAX_LIMIT
MIN_ABSTRACT_DEPTH
RULER_1 0.125 Cubic Angstrom
OUTPUT_RANK
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NOTICE:
  • MODE:
    1. Ligand file should be uploaded if the mode is Ligand Mode.
  • For Receptor File:
    1. Both Peptides and Nucleic Acids are avaliable for Cavity Server.
    2. ONLY PDB format is supported(example).
    3. The protein name should not contain @ ? + $ % * & ! ^, Otherwise it may lead to a mistake.
  • For Ligand File:
    1. ONLY MOL2 formate is supported. Here we suggest users using Openbabel to convert.
  • For Parameter Sets:
    1. SEPARATE_MIN_DEPTH: Default minimal depth of binding-site. Linkage between sub-cavity that do not reach this critical will be cut.
    2. MAX_ABSTRACT_LIMIT: Default abstract surface area. Increase this value if the real binding site is much larger than the detection result, and vice-versa.
    3. SEPARATE_MAX_LIMIT: Default surface area. Increase this value if the real binding site is much larger than the detection result, and vice-versa.
    4. MIN_ABSTRACT_DEPTH: Default abstract depth. Increase this value if the real binding site is much larger than the detection result, and vice-versa.
    5. RULER_1: Limt the minimum volume.
    6. OUTPUT_RANK: Limit the minimum score.



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