This is the main tutorial and help file for
PIDD: Database for Protein Inter-Atomic Distance Distribution
PIDD is a
dedicated database and structural bio-informatics system for distance based
protein modeling. The database is developed to host and analyze the statistical
data for protein inter-atomic distances based on their distributions in
databases of known protein structures such as in the PDB Data Bank. PIDD is
capable of generating, caching, and displaying the statistical distributions of
the distances of various types and ranges. The collected information can be used
to extract geometric restraints or mean-force potentials for protein structure
determination including NMR structure determination and comparative model
refinement.
Any users can
freely access and use PIDD for academic or industrial purpose without registrations
and charge. To
obtain better performance, Internet Explore 6.0 or above and Netscape 4.0
or above are suggested.
PIDD is a database providing
protein inter-atomic distance distributions. All residues and atoms involved
must be specified. For example, Cα in TYR and Cα in TYR separated by LYS in
sequence. PIDD allows the users to choose the distance type to be searched for
via simple menu selections. Typically, the users follow three selection steps: (i)
specify the two end residues and the number of separating residues; (ii) specify
the types of the two atoms in the two end residues, respectively and the types
of all separating residues; (iii) submit the query. The current version of PIDD
allows the users to specify up to 3 separating residues and handles one distance
type per query, but it can be used simultaneously by multiple users.
The system returns
with the distribution of the specified type of distances and displays it in a
graph. Because of the architecture of the database (see more details in
the system description), the distance distributions could be either instantly
processed in the distance database or computed on fly from the structural
database and stored into the distance database afterwards.
Pair wise distance
distribution of atoms in two adjacent residues respectively with separating
residues.
Cα in TYR and Cβ
in TYR without separating residues
1. Enter the
database webpage in the PIDD; Specify types of two residues where two atoms are
located in respectively, and also set separating resides at None; Click Go To
Next.
2. Specify
types of two atoms ; Click Submit.
3. Display the
results
Pair wise distance
distribution of atoms in two adjacent residues respectively without separating
residues.
Cα in ALA
and Cα in ALA separted by ALA
1. Enter the
database webpage in the PIDD; Specify types of two residues where two atoms are
located in respectively, and also set separating resides at 1; Click Go To Next.
2. Specify
types of two atoms and the type of residue between two residues where two atoms
are located in; Click Submit.
3. Display the
results
If you have
any suggestions, questions, or comments, please either leave a message in the
Guestbook or send an email to diwu@iastate.edu
Wu, D., Cui,
F., Jernigan, R., Wu, Z., PIDD: Database for Protein Inter-atomic Distance
Distributions, submitted, 2006
Author information goes here.
Copyright © 2006 Wu's Group. All rights reserved.
Revised:
03/29/06.