You can also calculate the area covered by the centre of a water molecule rolling over the surface of an exposed protein atom. Relative accessible surface area or relative solvent accessibility rsa of a protein residue is a measure of residue solvent exposure. Pops calculates accessible surface area for the whole protein, residues, or atoms. Accessible surface area and accessibility calculation for protein ver. Molecular surface representation tel aviv university. The relative accessible surface of some residues is more than 1. Protsa institute for biocomputation and physics of. Keywords for this software anything in here will be replaced on browsers that support the canvas element. This algorithm uses a sphere of a particular radius to probe the surface of the. I want to extract the coordinates of the surface atoms i. Naccess is a stand alone program that calculates the accessible area of a molecule from a pdb protein data bank format file. An open source c library for solvent accessible surface area calculations simon mitternacht university library, university of bergen postboks 7808, 5008 bergen, norway simon.
The boundary between ones and zeros is the solvent accessible surface sas, that is where the center of the probe sphere rolling over the atoms can reach. It can calculate the atomic and residue accessiblities for both proteins and nucleic acids, and is available for free from this site for researchers at. Categories tips tags pdb, protein, pymol, visualization. The contact surface is the surface traced out by the vdw surfaces of the water atoms when in contact with the protein. Using the surface display mode, pymol doesnt show the solvent accessible surface, rather it shows the solvent protein contact surface. Hi all i doing one task with pymol where i need to calculate solvent accessible surface area for individual residues numbers. Could any one please suggest command or script to do it. Application a new pymol plugin in quantitative structure. Pdbe accessible and buried surface area the view interface option, using jmol, from the interface details page, gives a excellent indication of the meaning of these terms. Atomic and residue areas the latter simulated with a single sphere centered at the calpha atom for amino acids and at the p atom for nucleotides have been optimized versus accurate allatoms methods naccess. Although the exact quantitative relation between surface area and free energy is elusive, the sasa can be used to compare different molecules or different conformations of the same molecule, or for example measure the surface that is buried due to oligomerization. A plugin for the pymol molecular visualization system that analyzes proteindna binding interfaces by comparing the solvent accessible surface area of the complex against the free protein and free dna.
Calculate accessible surface area and accessibility of protein. Both asa and maxasa are commonly measured in to measure the relative solvent. How extract coordinates of surface atoms of a protein from. Five cool features in pymol that you may have missed related. Pymol is a powerful and comprehensive molecular visualization product for rendering and animating 3d molecular structures. Solvent accessible surface area md simulations at fsu. The solvent accessible surface area sasa of a molecule gives a measure of the contact area between molecule and solvent.
Surface area accessibility calculations identify which residues are solvent exposed and which residues are buried, contributing to the hydrophobic stabilization of protein structure. Accessible surface area an overview sciencedirect topics. Solvent accessible surface area heres how you analyze solvent accessible surface area, from here on out abbreviated to sasa. The plugin provides three distinct threedimensional visualization modes to highlight interactions with dna bases and backbone, major and minor groove, and with atoms of different pharmacophoric. Masanda, vesna rastijab a department of chemistry, vidya bharati mahavidyalaya, amravati, maharashtra 444 602, india b department of chemistry, faculty of agriculture, josip juraj strossmayer university of osijek, osijek, croatia article info. Popscomp looks at the change in asa for all pairwise combinations of molecules in the structure. Measurement of asa is usually described in units of square angstroms. A surfaceareashp returns the total surface area of 3d alpha shape shp, including the surface area of any interior voids in the alpha shape.
Use the create binding site surfaces panel, which you can open with workspace surface binding site create binding site surfaces prior to the 20164 release. Waters can touch residues at the surface of a protein. Pymol can show solvent accessible surfaces using the dot or sphere representations. Sasa is the surface area of a biomolecule that is accessible to a solvent. Protsa will generate, for your protein of interest, an ensemble of unfolded conformations, and will calculate the average solvent accessible surface area sasa of each atom and residue in the ensemble. Pymol molecular graphics system pymol need help to get. Calculating solvent accessible surface area using command line tools. See help pages if you need help with using the wiki pops and popscomp are tools for rapid calculation of solvent accessible surface area sasa from pdb files.
I use mark gersteins calcsurface program available online at helix systems server of nih. Pops is a fast algorithm to calculate accessible surfaces areas at atomic default and residue coarse grained level. Now i want to calculate the solvent accessible surface area sasa of polymer. Molecular surface representation representing a protein by its molecular surface representation helps us in the study of protein folding, in prediction of biomolecular recognition, detection of drug binding cavities and molecular graphics. Calculation of solvent accessible surface areas, atomic solvation energies and. So, as a concept we calculate the area of every sub unit such as chain a, b, c etc as well as total area of the protein. Pydescriptor is a new script implemented with the commonly used visualization software pymol for. Calculating solvent accessible surface area using command. Estimating solvent accessible surface area of a protein. A new pymol plugin for calculating thousands of easily understandable molecular descriptors vijay h. The quickest and easiest way to generate electrostatics is with the inbuilt vacuum electrostatics tools. The solvent accessible surface area is usually defined as the surface traced out by the center of a water sphere, having a radius of about 1. By changing its entries you can calculate surface areas for only specific atom types or switch the program to calculate solvation energies with different asp sets. Specific recognition of dna by proteins is a crucial step of many biological processes.
Application a new pymol plugin in quantitative structuretoxicity relationship study of pesticides. Video description in this video, we present a quick technical on how to calculate solvent accessible surface area of biological macromolecules using a commandline software tools. In the present work, we present a new pymol plugin, pydescriptor, which has capacity to calculate 11,145 easily understandable molecular descriptors. The current pisa program does not allow the interfacing residues. The noninterfacing atoms which are solvent accessible, are coloured light blue and dark blue for the two molecules respectively. The solvent excluded surface is the boundary of where the surface of the rolling probe sphere can reach. I would be interested in the accessible surface area of an amino acid. The noninterfacing atoms which are solvent accessible, are coloured light blue and dark blue.
I want to extract the coordinates of the atoms that are on the surface of protein and by that i dont mean the set of atoms of surface residues because that set may contain atoms that are deeply buried inside the protein. Here, we present a versatile software tool and web server for the calculation of contact surface areas, as well as buried surface areas and solvent accessible surface areas sasa for different types of biomolecules, such as proteins, nucleic acids and small organic molecules. Calculation of accurate interatomic contact surface areas. You can set the distance from the ligand in this panel. An open source c library for solvent accessible surface. The accessible surface area of the protein is calculable from a set of coordinates which measures the thermodynamic interaction between protein and water. All you need to provide is the sequence of your protein using the form below. Apbs electrostatics in pymol the pymol molecular graphics software package provides support for both the execution of apbs and the visualization of the resulting electrostatic potentials. In general the program is run on your local computer and there are installers for os x, linux and windows. But when i use pymol to calculate sasa and insert my pdb file. Solvent accessible surface area approximations for rapid. Five cool features in pymol that you may have missed. To start quantifying this, pymol has tools for calculating solvent accessibility for example.
Pops a fast algorithm for solvent accessible surface. Molecular surface algorithms tom goddard oct 14, 20. Additionally pdbsum and pdbepisa can estimate solvent accesible surface area. Note that the accessibility is assessed in the context of the objects that the selection is part of. Pdb format files will use a naccess compatible vdw radii lookup table, while mol2 formats will use the same vdw radii used in chimera. Pdiviz is a plugin for the pymol molecular visualization system that analyzes proteindna binding interfaces by comparing the solvent accessible surface area of the complex against the free protein and free dna. Generally, a sphere of water is assumed to be the solvent molecule with a radius 1. Calculating solvent accessible surface areas sasa is a. Calculation of accurate interatomic contact surface areas for the. Now i want to calculate its solvent accessible surface area sasa. Calculating solvent accessible surface area using standalone. Therefore, there is need for introduction of easily understandable molecular descriptors. Is there any webtool or program for sasa solvent accessible area.
The accessible surface area or solventaccessible surface area is the surface area of a biomolecule that is accessible to a solvent. Areaimol calculates the solvent accessible surface area by generating surface points on an extended sphere about each atom at. Accessible surface area calculations are based on finite element analysis. Any suggestions or comments would be highly appreciated. The solvent accessible surface area sasa is a geometric measure of this exposure, and therefore a dependency exists between sasa and environment free energy 33, 34. The solvent accessible surface area is the area of the surface swept out by the center of a probe sphere rolling over a molecule atoms are. The accessible surface area asa or solventaccessible surface area sasa is the surface area of a biomolecule that is accessible to a solvent. Calculation of solvent accessible surface area of nonhydrogen.
Estimating solvent accessible surface area of a protein youtube. Each atom can potentially be touched by water, and the area of an atom on the surface that can be touched by water is called the accessible molecular surface, or solvent exposed area. Pymol is a commercial product, but we make most of its source code freely available under a permissive license. Pymol can only show solvent accessible surfaces using the dot or sphere representations. It is a new cheminformatics tool which transforms a variety of structural features and local environment.
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