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Structure ID
PDB ID
Fetch&View/Chime
Rscript
Mscript
BCL
rmsd_in
rmsd_out
dihedral
SAS
CaMap
DistMap
inter energy
inter dist
 
 
 
Cn3D

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Structure identify

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1
Identify if a sequence accession number is linked to a PDB file (menu: family)
Input: list of accession numbers from sequence databases
Output: list of corresponding PDB accession numbers
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2
Identify if a sequence is described by a PDB file (menu: family)
Input: amino-acid sequence
Output: corresponding PDB accession numbers of the closest sequences
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Go to page bottom Identify the name of a protease from its PDB accession number (menu: family)
Input: list of PDB accession numbers
Output: list of corresponding names, organisms and other associated accession numbers
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Structure viewer

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1
Import structure files and display molecules with Chime (menu: fetch&view)
Input: PDB accession numbers
Output: display of the 3D active image of the molecule with Chime.
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2
Make scripts for Rasmol/Chime (menu: family )help for scripts
Input: PDB accession number, click actions
Output: display molecule and apply the scripts
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3

Make nice view from Molscript (menu: family)
Input: PDB accession number, click actions
Output: display molecule and apply the scripts

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4

Make scripts for Insight-MSI (menu: family)
Input: PDB accession number, click actions
Output: BCL script

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Structure superimposition

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1

RMSD between two superimposed structure residue sets(menu: family)
Input: PDB accession numbers, chain identifiers, domains or residue sets
Output: rmsd

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2

RMSD between two structure sets after superposition of two other sets(menu: family)
Input: PDB accession numbers, chain identifiers, domain or sets of superposed residues and compared residues
Output: rmsd

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Structure analysis

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1

Dihedral angle analysis (menu: family)
Input: set of PDB accession numbers
Output: diagrams and histograms

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2

Solvent accessible surface area (menu: family)
Input: sets of PDB accession numbers and operators
Output: list of residue positions, 1D, 2D and 3D-structure display

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3
Ca-Ca distance map (menu: family)
Input: PDB accession numbers
Output: list of residue positions, 1D, 2D and 3D-structure display
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4
Distance map (menu: family)
Input: sets of accession numbers and operators
Output: list of residue positions, 1D, 2D and 3D-structure display
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Residue set maker

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1
Make a set of residues according to type or geometry constraints (menu: family)
Input: PDB accession number, constraints (distance, surface, dihedral...)
Output: set of positions to copy and paste.
Go to page bottom Apply logic operator on two sets of positions (menu: family)
Input: PDB accession number, 2 set of positions
Output: set of positions to copy and paste.
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Analysis of mutation effect on energetics (local use only of licenses)

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1
Predicted effect of mutations on energetics from the same fold (menu: family)
Input: PDB accession number, mutation
Output: energetics
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Analysis of domain-domain interaction

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1
Energy estimation of interaction (menu: family)
Input: PDB accession number, domain 1, domain 2 (inter or intramolecular)
Output: contact surface parameters, energies, energy maps
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2
Distance map (menu: family)
Input: PDB accession number, domain 1, domain 2 (inter or intramolecular)
Output: distance map on the both components
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3
Interaction by reference to atlas(menu: family)
Input: PDB accession number, domain 1, domain 2 (inter or intramolecular)
Output: energetic and surface graph
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4
Predicted effect of mutations on interaction energetics from the same fold (menu: family)
Input: PDB accession number, domain 1, domain 2 (inter or intramolecular), mutation
Output: energetics
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Docking (local use only of licensed software)

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1
Docking with AutoDock (menu: family)
Input: PDB accession number, target, coordinates of ligand atoms
Output: Atomic coordinates of the predicted structure by mail and local temporary database
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2
Docking with Discover (menu: family)
Input: PDB accession number, target, coordinates of ligand
Output: Atomic coordinates of the predicted structure by mail and local temporary database
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3
Fast docking in the sphere world (menu: family)
Input: PDB accession number, target, coordinates of ligand
Output: Atomic coordinates of the predicted structure by mail and local temporary database
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Prediction of metal ion binding sites (local use only)

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1
Prediction of metal ion binding sites with Valence (Nayal & Di Cera)(menu: family)
Input: PDB accession number, ion type
Output: Binding site list, 3D-display
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Threading of sequences (local use only)

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1
Prediction of 3D-structure from the sequence (menu: family)
Input: sequence or Swiss-Prot accession number
Output: Atomic coordinates of the predicted structure by mail and local temporary database
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Thierry Rose, PhD and Enrico Di Cera, MD
Department of Biochemistry and Molecular Biophysics
Washington University School of Medicine
Saint Louis, MO, U.S.A.

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