Hi all i doing one task with pymol where i need to calculate solvent accessible surface area for individual residues numbers. Access to the solvent accessible surface area information for the model of calbindin in the open conformation is. 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. Calculating solvent accessible surface area using command.
Methods for calculating solvent accessible surface area sasa image credit. Although there are many programs available for this calculation, there are no freestanding, opensource tools designed for easy toolchain integration. Accessible surface area and accessibility calculation for. 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.
The surface potential is also straightforward to visualize. We compared the results against naccess, a reference software for sasa calculation hubbard and thornton, 1993. On methods for determining solvent accessible surface area. 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. Software for deep analysis of pdb structures and mechanism. Specifically, while the program will sometimes tell you if you have asked for information on a residue that does not exist in a given protein, it will sometimes just print the information, with the surface area equal to 0. Manual calculation of descriptors like 3dmorse, whim, bcut, and similar complex or esoteric 5 descriptors was a very time consuming and laborious process 1,912,15,16. Which python 3 library is recommended for a solvent. In general the program is run on your local computer and there are installers for os x, linux and windows. Feb 18, 2016 calculating solvent accessible surface areas sasa is a runofthemill calculation in structural biology.
Sep 08, 2016 surface area is the area covered by solvent. Mapping hydrophobicity on the protein molecular surface at. Hi everyone, i have a pdb file that contains a single protein information. The shrake and rupley algorithm 38 involves the testing of points on an. Any suggestions or comments would be highly appreciated. Need to look at the pymol source code to determine the exact method it uses.
The solute molecule is represented by a set of interlocking spheres of. Calculation of accurate interatomic contact surface areas. The solvent accessible surface area sasa of a molecule gives a measure of the contact area between molecule and solvent. Residues are considered to be solvent exposed if the ratio value exceeds 50% and to be buried if the ratio is less than 20%, marked as o and i respectively in the last column.
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. Calculation of solvent accessible surface area of nonhydrogen atoms for which all asp1. Calculation of accurate interatomic contact surface areas for. Close, but it depends on whether you want the surface area of the residues alone, or in the context of the molecule. How extract coordinates of surface atoms of a protein from a. Were going to use our trustly alanine dipeptide trajectory for this calculation, but in a realworld situtation youll probably want to use a more. Per residue solvent accessible surface area calculator.
There is a new library called freesasa written by simon mitternacht in c. Solvent accessible surface area heres how you analyze solvent accessible surface area, from here on out abbreviated to sasa. An open source c library for solvent accessible surface area calculations simon mitternacht university library, university of bergen postboks 7808, 5008 bergen, norway simon. 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. For more information, please visit knowledge base article 37 or view our documentation on running jobs from the command line. A surfaceareashp,regionid returns the surface area of a region of the alpha shape. Note that the accessibility is assessed in the context of the objects that the selection is part of. Developed at ucl by simon hubbard and janet thornton, this program calculates absolute and relative surface accessibilities of protein and nucleic acid structures. Feb 18, 2016 the solvent accessible surface area sasa of a molecule gives a measure of the contact area between molecule and solvent. Assigning a numerical value for accessibility requires a method of integration over the surface area. There are many different methods for estimating solvent accessible surface area for proteins in their unfolded states.
Both asa and maxasa are commonly measured in to measure the relative. Protsa will generate, for your protein of interest, an ensemble of unfolded conformations, and will calculate the average solventaccessible surface area sasa of each atom and residue in the ensemble. Solvent accessible surface area sasa calculation in this example, well compute the solvent accessible surface area of one of the residues in our protien accross each frame in a md trajectory. The quickest and easiest way to generate electrostatics is with the inbuilt vacuum electrostatics tools. To use any of these scripts simply use the following instructions. Can anyone recommend a server for calculating solvent. Accessible surface area is often used when calculating the transfer free energy required to move a biomolecule from aqueous solvent to a nonpolar solvent such as a lipid environment. Both asa and maxasa are commonly measured in a 2 \displaystyle \mathrm \aa 2. The random coil value of a residue x is the average solvent accessible surface area of x in the tripeptide glyxgly in an ensemble of 30 random conformations. Solvent accessible surface area approximations for rapid and. Keith callenberg most of these methods are based on the shrakerupley algorithm 1 which creates many points on the surface of each heavy atom and determines whether each point is occluded or exposed to solvent. Pymol doesnt show the solvent accessible surface, rather it shows the solventprotein contact surface. 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 spheres of varying radii.
The schrodinger suite of software has a large number of applications for a variety modeling, analysis and computational tasks. 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. The lcpo method is also used when calculating implicit solvent effects in the molecular dynamics software package amber. Solvent accessible surface area md simulations at fsu. Prediction and analysis of surface hydrophobic residues in.
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. The software naccess was used to calculate asa for all atoms in pdb file. Accessible surface area an overview sciencedirect topics. Could any one please suggest command or script to do it. Methods for calculating solvent accessible surface area. Pymol molecular graphics system pymol need help to get. Areaimol calculates the solvent accessible surface area by generating surface points on an extended sphere about each atom at.
The contact surface is the surface traced out by the vdw surfaces of the water atoms when in contact with the protein. This is a discrete approximation not an exact calculation. Solvent accessible surface area sasa calculation mdtraj 1. Introduction of solventaccessible surface area in the.
Pops a fast algorithm for solvent accessible surface areas. Feb 21, 2009 lee and richards presented the first algorithm for calculating the solventaccessible surface area sasa of a molecular surface. Which server to use for volume and accessible surface area. You can use pdbsum and pdbepisa servers for calculating accessible surface area and buried surface area and castp server for finding pockets within your protein molecule.
Solvent accessible surface area approximations for rapid. Lee and richards presented the first algorithm for calculating the solventaccessible surface area sasa of a molecular surface. Now i want to calculate the solvent accessible surface area sasa of polymer. Also, which pdb file do i have to use as an input for these softwares. All of the scripts listed on this page come prebundled with the latest schrodinger software release. Accessible surface area and accessibility calculation for protein ver. I have ran molecular dynamic simulation for mutated prion protein for 50 ns using gromacs software.
In this article, we compare eight methods, assessing whether or not they lead to different estimates of total accessible surface area as well as their impact on relationships with thermodynamic variables. A precise representation of the spatial distribution of hydrophobicity, hydrophilicity and charges on the molecular surface of proteins is critical for the understanding of the interaction with small molecules and larger systems. Additionally pdbsum and pdbepisa can estimate solvent accesible surface area. The programs output is both, quantitative a single wholepdb value and qualitative pdb surface is colored by scaled peratom values. Generally, a sphere of water is assumed to be the solvent molecule with a radius 1. Pdbe accessible surface area calculations are based on finite element analysis numerical analysis calculation as a full exact analysis using integrals is quite complex even for something like water. It takes zsections through the molecule, tracing a solvent accessible path around the molecule in each section. 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. Check the solvent accessible surface and color by potential on sol. An open source c library for solvent accessible surface area calculations mittinattenfreesasa.
Nov 01, 2017 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. Research article introduction of solventaccessible surface area in the calculation of the hydrophobicity parameter log p from an atomistic approachtakashi masuda, a takahiro jikihara, a katsuhiko nakamura, a atsuomi kimura, a. Hi jianghai, some of these questions have been answered by warren. Relative accessible surface area or relative solvent accessibility rsa of a protein residue is a measure of residue solvent exposure. The random coil value of a residue x is the average solventaccessible surface area of x in the tripeptide glyxgly in an ensemble of 30 random conformations. Pymol surface i think the gaussian surfaces, sum of balls surface, and pymol surfaces all look similar, so im guessing pymol is the same kind of surface. All you need to provide is the sequence of your protein using the form below.
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. 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. Pops is a fast algorithm to calculate accessible surfaces areas at atomic default and residue coarse grained level. The solvent accessible surface is just the boundary of the union of atom balls that have their radius increased by the probe radius typically 1. Pdbbased calculation of surface burial, electrostatic energy and solvation energy for proteins and nucleic acids and proteinprotein proteinrna and proteindna complexes. If your protein is globular, you can measure the diameter in pymol and calculate its volume. The representation of hydrophobicity is rarely done at atomlevel, as this property is generally assigned to residues. The program can also be used in conjunction with the ligplot program to provide information on buried and accessible residues.
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