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For details of the methodology, see the papaer:

"Comprehensive classification and diversity assessment of atomic contacts in protein-small ligand interactions."
Kota Kasahara, Matsuyuki Shirota, Kengo Kinoshita
J Chem Inf Model. 2013 Jan 28;53(1):241-8.

CONTENTS.


Complex analyzer

a. Input form for a query

A query complex can be specified from this form.

Please input PDB-ID and 3-letter ligand code as following: "[PDB-ID]_[3-letter code]" , e.g., "3dfr_TMX".

If our database does not have the complex what you want to see, use upload form.

b. Upload form for a query

The query complex can be uploaded as a PDB file. 3-letter code of a ligand molecule has to be specified.

c. Jmol viewer

GIANT is powered by Jmol for the interactive structure viewer.

d. Check boxes for ppearances of protein entire structure

These check boxes provide manipulation of appearances of protein entire structures in the two ways: ball&sticks, and ribbon

e. Residue list

The list provides information about each amino acid residues that interacting with the ligand.

IDID number of the amino acid residue.
TypeType of the amino acid residue (one of the 20 kinds of regular amino acids).
InteractionsNumber of interactions involving the amino acid residue.

f. Ligand atom list

The list provides information about each ligand atoms that are recognized by the receptord.

IDID number of the ligand atom.
NameName of the ligand atom.
TypeType of the ligand atom, defined by Tripos forcefield.
InteractionsNumber of interactions involving the ligand atom.

g. Interaction list

The table shows basic information about each interaction, that means a contacting pair of a amino acid fragment (triplet of atoms) and a ligand atom.
Intrct
IDID number of the interaciton.
Residue
TypeType of the amino acid residue.
IDID number of the amino acid residue.
TripletNames of the three atoms composing the fragment. The first atom is interacting with the ligand atom.
Ligand
IDID number of the ligand atom.
TypeType of the ligand atom.
Pattern
IDID number of the interaction pattern. It is link to the Pattern Viewer.
Prob.Probability density of occurence of interactions at this position when the pair of the fragment and the ligand atom are interacting.
FamilyNumber of protein families using the interaction pattern in our dataset. A protein faimily were defined as an single-linkage cluster of protein sequences.
FreqNumber of complexes using the interaction pattern in our dataset.

Users can download this table as comma separated ascii file (.csv) from underneath the viewer..


Pattern viewer

a. Select boxes specifying a type of a amino acid fragment and a ligand atom.

User can jump to Pattern Viewer pages by specifying the types from these boxes and clicking "load" button.

b. Jmol viewer

GIANT is powered by Jmol for the interactive structure viewer.

Meshes means spatial distributions of interaction patterns. The positions inside the meshes are statistically relevant positions for interacting a ligand atom.

Three atoms shown in balls and sticks indicate the fragment of amino acid.

When users jumped from Complex Anlyzer, the clicked interaction pattern shown as red.

c. List of interaction pattern

IDID number for the interaction pattern
PiProbability of the interaction pattern, or the Gaussian element, in the Gaussian mixture model.
FamilyNumber of protein families using the interaction pattern in our dataset.
FreqNumber of complexes using the interaction pattern in our dataset.
CmpxLink to the list of protein-ligand complexes using the interaction pattern.

d. Ligand sttatistics and a list of complexes which has the specified interaction pattern

Ligand Statistics
Ligand3-letter ID of ligands.
CountThe number of interactions with the ligand in the pattern.
List of complexes
EntryIdID for the complex.
Interaction IDID for the interaction with the specified pattern.
ProbabilityProbability of the interaction.