Serine protease: Structure Analyzer

We are still working on this page. Tools will be added and opened gradually until the end of August, the date of the first complete version of this web site. You can find more about the schedule in "what's next ?"

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

Click the yellow button in the menu above or the yellow bullet in the descriptive menu below. A Red bullet means the corresponding page is not yet released. If you click on it you will find an estimate of the release date and its current state of development.

	Structure identify
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
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

	PDB code Identify
	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

	Structure viewer
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.
2	Make scripts for Rasmol/Chime (menu: family )help for scripts Input: PDB accession number, click actions Output: display molecule and apply the scripts
3	Make nice view from Molscript (menu: family) Input: PDB accession number, click actions Output: display molecule and apply the scripts
4	Make scripts for Insight-MSI (menu: family) Input: PDB accession number, click actions Output: BCL script

Structure superimposition

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

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

Structure analysis

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

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

	Residue set maker
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.
	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.

	Analysis of mutation effect on energetics (local use only of licenses)
1	Predicted effect of mutations on energetics from the same fold (menu: family) Input: PDB accession number, mutation Output: energetics

	Analysis of domain-domain interaction
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
2	Distance map (menu: family) Input: PDB accession number, domain 1, domain 2 (inter or intramolecular) Output: distance map on the both components
3	Interaction by reference to atlas(menu: family) Input: PDB accession number, domain 1, domain 2 (inter or intramolecular) Output: energetic and surface graph
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

	Docking (local use only of licensed software)
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
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
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

	Prediction of metal ion binding sites (local use only)
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

	Threading of sequences (local use only)
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

[HomePage] [Sequence Index] [Sequence Analyser] [Mutations] [Evolution] [Tour-Tutorial] [Help]
[Structure Index] [Structure Analyzer] [Ligands] [Function][About] [Contact_us][Setup][Search] [Links]

Go to the Department of Biochemistry and Molecular Biophysics

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.