ANOLEA (Atomic Non-Local Environment Assessment)

ANOLEA

(Atomic Non-Local Environment Assessment)

Francisco Melo and Ernest Feytmans.

This server was originally developed at:
Unité de Recherche en Biologie Moléculaire (URBM)
The University of Namur, Belgium.

Now it is running at:
Laboratorio de Bioinformática Molecular
Pontificia Universidad Católica, Chile.

Please send any comments and enquiries to: 

   Francisco Melo Ledermann

   P. Universidad Católica de Chile          :   Tel: +56-2-2686 2279
   Laboratorio de Bioinformática Molecular   :   Fax: +56-2-2475 0051
   Alameda 340, Santiago.                    :   E-mail: fmelo@bio.puc.cl
   Santiago. Chile.                          :

What is ANOLEA ?

ANOLEA (Atomic Non-Local Environment Assessment) is a server that performs energy calculations on a protein chain, evaluating the "Non- Local Environment" (NLE) of each heavy atom in the molecule. The energy of each pairwise interaction in this non-local environment is taken from a distance-dependent knowledge-based mean force potential that has been derived from a database of 147 non-redundant protein chains with a sequence identity below 25% and solved by X-Ray crystallography with a resolution lower than 3 Å.

We strongly recommend to read the help provided for each mandatory parameter when using ANOLEA for the first time.



Assessing Protein Structures

The assessment of protein structures is a delicated matter. Currently, there is not a single method able to consistently and accurately predict the three-dimensional structure of a protein. Moreover, our lack of knowledge about protein folding and stability makes difficult to develop such a method.

Similarly, there is no single method able to consistently and accurately predict the errors in a protein structure. For that reason, we strongly recommend to use as many as possible different methods when assessing a protein structure (below we provide links to some well- known and widely used methods). Different methods use different approaches, thus they can complement to each other. In that way, you can have more confidence about the predicted error of specific regions in the protein.



A List of 'Well-known' and 'Widely-used' Methods to Assess Protein Structures

ANOLEA FORM

Job title (optional) :

Window Average: (Help)

Threshold to define a high energy amino acid : ( Help)

Protein chain information (mandatory): ( Help)

Please, in the box below, write the sequence of all the chain identifiers of your protein. In first place put the chain on which you want to perform the calculations. The non-local energy profile will be performed only on the chain indicated by the first chain identifier of the sequence supplied in the box below, but considering all the atoms of the other chain identifiers. If you are submiting a monomeric protein you must write the chain identifier if there is one. If there is not a chain identifier, please leave this box free. We strongly recommend to read the help provided for this issue when using ANOLEA for the first time.

Chain names:

Indicate the name of the PDB file that contains the coordinates. Use this field to browse your file (recommended) or paste the "ATOM" section of your PDB file in the text area supplied below. This parameter is mandatory. Do not paste anything if you have indicated a filename in the box:

File Upload: Give the name of the PDB file in your system (it must be a text file not encoded !)

Warning: All heteroatoms supplied will be removed and will not be considered in the calculations.

Have you the CHIME plug-in installed ?: (Help)

If you have not installed MDL CHIME on your computer, you can download it from here (MDL CHIME is free and we recommend to use it to analyze the results of the calculation). A complete information about MDL CHIME capabilities is available here

MDL CHIME requires Netscape 2.0 or later (depending on the platform you are using)

How do you want the output ?:

Bibliography

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