What Does ProtFract Offer

Protfract server offers two classes of broad services: services meant for calculating many protein interior fractal-properties and services meant for calculating protein exterior fractal-properties.

Analysis of protein interior fractal-properties: ProtFract calculates the self-similarity in inhomogeneous[1] distributions of mass[2], hydrophobicity and polarizability with fractal dimension (FD). Such characterizations help in quantifying the ‘unused-hydrophobicity’ within a protein (calculated by evaluating (abs(hydrophobic-FD - mass-FD))[3]. Alongside these, the correlation-dimension(CD)-based analyses, quantify the self-similarity in dependencies (alternatively, correlations) amongst biophysical properties[4]. Under ProtFract CD-suit, one obtains the information regarding the extent of symmetry in the dependence amongst various structural parameters; for example, extent of self-similarities in the dependencies amongst - dipole moment distributions, hydrophobic residues, chiral centre distributions, aromatic residue distributions, charged residue distributions, etc.. Furthermore, one obtains information regarding extent of self-similarity in possible interactions between aromatic residues and positively charged residues.

Analysis of protein exterior fractal-properties: Fractal dimensions can quantify the symmetry in roughness profile of protein surfaces[5]. Roughness of protein surfaces introduces an additional complexity in investigations related to drug-discovery. This extra bit of information can be immensely helpful when one considers it in concurrence with geometry of the local shape of protein exterior concerned. Indeed, past studies have established the utility of surface-FD in the context of studying protein-ligand interactions[6], protein-protein interactions[7] and other cases[8-10]. ProtFract, therefore presents the information regarding surface-roughness, as measured with FD. Alongside this, since correlation dimension (CD) amongst surface atoms can provide valuable insights about various types of biophysical investigations[11] into surface properties and recognition process, ProtFract presents information about surface atom CD for varying probe radii.

Upon submitting query in PDB format, two types of surface corrugation information can be obtained. In the first, information regarding roughness of protein surface is provided. Herein, on obtains the information regarding surface roughness of an entire protein, alongside, information about surface roughness of a patch of protein surface. While the former (information regarding roughness of entire protein surface) can help the user in drawing meaningful inference while comparing surface properties of two sets of proteins; the later (that is, roughness of a patch of protein surface) can be very helpful for active site roughness calculation and other related investigations. The other kind of ProtFract exterior information deals with symmetry of correlations amongst surface atoms when probed with varying probe radii. However, since ProtFract employs the program ‘Surface Racer’[12] to calculate accessible surface area and molecular surface area, and since the program ‘Surface Racer’ does not work on submitted queries containing disconnected structures (implying that the structures cannot be bridged by the probe sphere), ProtFract will not be able handle such cases. Furthermore, we request the users to suitably remove the Hydrogen atom information before submitting the query for exterior calculations.

References:
[1] Banerji A, Ghosh I (2009) A new computational model to study mass inhomogeneity and hydrophobicity inhomogeneity in proteins. Eur Biophys J 38:577-587
[2] Enright MB, Leitner DM (2005) Mass fractal dimension and the compactness of proteins. Phys Rev E 71:011912
[3] Banerji A, Ghosh I (2009) Revisiting the myths of protein interior: studying proteins with mass-fractal hydrophobicity-fractal and polarizability-fractal dimensions. PLoS One 4(10):e7361
[4] Banerji A, Ghosh I (2011) Fractal symmetry of protein interior: what have we learned? Cell. Mol. Life Sci. DOI 10.1007/s00018-011-0722-6
[5] Lewis M, Rees DC (1985) Fractal Surfaces of Proteins. Science. 230:1163-1165.
[6] Pettit FK, Bowie JU (1999) Protein surface roughness and small molecular binding sites. J Mol Biol 285:1377-1382.
[7] Aqvist J, Tapia O (1987) Surface fractality as a guide for studying protein-protein interactions. J Mol Graph 5:30-34.
[8] Kopelman R (1988) Fractal reaction kinetics. Science 241:1620-1626.
[9] Chakravarty S, Wang L, Sanchez R (2005) Accuracy of structure-derived properties in simple comparative models of protein structures. Nucl Acid Res 33(1):244-259.
[10] Dewey TG (1994) Fractal analysis of proton exchange kinetics in lysozyme. Proc Natl Acad Sci USA 91:12101-12104.
[11] Choi JH, Lee S (2000) Correlation between the roughness degree of a protein surface and the mobility of solvent molecules on the surface. J Chem Phys 113(15):6325-6329.
[12] Tsodikov, O. V., Record, M. T. Jr. and Sergeev, Y. V. (2002). A novel computer program for fast exact calculation of accessible and molecular surface areas and average surface curvature. J. Comput. Chem., 23, 600-609.