AREAIMOL FREE DOWNLOAD

The area calculations also depend critically upon various parameters, such as the probe radius taken to be 1. There is also a breakdown of accessible area differences by residue, chain and for the whole molecule. Peter Briggs, Ian Tickle. The first area calculation will be for the oligomer, the second will be for the monomer. Multiple isolated surfaces could represent any combination of:. For each isolated area of surface identified, the program reports the number of atoms, the total accessible area and the centre of mass.

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Improvements to AREAIMOL code

The maximum size of protein that the program can handle is hardcoded in the parameter MAXNET in the source code file areaimol. Task for computing various types of contacts in protein structures. A number of simple tests were performed to assess the algorithms and compare their performance, as implemented in the two programs.

If the identity is the only operation that has been entered or if P1 symmetry is specified then a warning may appear, but this can be ignored unless you are not in P1 symmetry. Atoms which are not included in the comparison are ignored in the output. The solvent accessible surface is defined as the locus of the areiamol of a probe sphere representing the solvent molecule as it rolls over areeaimol Van der Waals surface of the protein illustrated for a simple case in figure 1.

These individual areas are then used to obtain an analysis of the total accessible area for each residue, chain and for the whole molecule. The difference in accessible area on each atom is then calculated and the overall area differences analysed.

Accessible areas or area differences for individual atoms can be written to wreaimol pseudo-PDB output file. Add or change areaikol atom type and associated Van der Waals radius recognised by the program.

AREAIMOL (CCP4: Unsupported Program)

Note also that the program does not check that the entries given are adeaimol residue names, or if any are repeated. This mode compares the difference in accessible area due to the presence of intermolecular contacts, e.

Here residue n represents a three-character residue name e. If the identity is the only operation that has been entered or if P1 symmetry is specified then araimol warning may appear, but this can be ignored unless you are not in P1 symmetry.

CCP4 Newsletter: accessible surface area calculations

Maximum residue number is Atoms belonging to any of the named residues will be ignored in the area calculations, and will not be written to the output Brookhaven file. The contact area is defined as the area on the Van der Waals surface of an atom that can be contacted by a sphere of the given probe radius see figure 2 above for a schematic representation of the contact area.

Only one set of coordinates areaimil input, and two separate area calculations are carried out the first treating waters as solvent, i. This mode compares the difference in accessible areainol for two similar molecules, e. This is summarised in a table with the following quantities:.

Ageaimol residue n represents a three-character residue name e. Atoms which are not included in the comparison are ignored in the output. Accessible areas or area differences for individual atoms can be written to a pseudo-PDB output file. The number of symmetry operations that the program can handle is hardcoded in the parameter MAXSYM in the source code file areaimol.

Add or change an atom type and associated Van der Waals radius recognised by the program. The van der Waals' radii used for non-hydrogen atoms are therefore modified to account for the implicit presence of hydrogens.

P2 1 2 1 2 1areaiimol International Tables number, or as a series of symmetry operations e. You may use up to 69 symmetry operations when looking for metal-ligand or intermolecular contacts. Here residue n represents arwaimol three-character residue name e. Two input coordinate files are required, and areaimlo separate area calculations are carried out, one for each set of coordinates. There are four possible modes of operation, specified by one of the subkeywords below. Effects of using different van der Waals' radii SURFACE Hydrogen atoms are not considered individually in the calculations because it is not usual for them to be included in coordinate files describing the protein atom positions.

Comparison of SURFACE and AREAIMOL for accessible surface area calculations

Choice of spacegroup or list of operators required if looking for metal-ligand or intermolecular contacts. Note also, areqimol the solvent accessible surface is distinct from the molecular surface, which is the locus of the inward-facing point of the probe sphere the sum of the contact and re-entrant surfaces.

The effect of intermolecular contacts which will reduce the accessible area can be included using the SMODE keyword which generates symmetry-related copies of the original molecule by applying the symmetry operations supplied with the SYMMETRY keyword and the TRANS keyword which areaimlo apply linear combinations of primitive lattice vectors to the symmetry-related molecules to generate further copies.

The default radius is 1.