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Schaum outline of programming with fortran 77 pdf viewer
Schaum outline of programming with fortran 77 pdf viewer






schaum outline of programming with fortran 77 pdf viewer

2015a), we report on the Tangent Sphere (TS) and Cutting Plane (CP) methods - two complementary methods to quantify, in a size-independent manner, the degree of ligand binding site (LBS) burial in a protein receptor - and their applications. The degree of ligand burial depth gives an indication of a receptor protein’s flexibility, as the extent of receptor conformational change required to bind a ligand is thought to vary directly with depth of burial in the bound state.

schaum outline of programming with fortran 77 pdf viewer

Keywords: protein-ligand interactions ligand burial ligand binding site burial protein centroid cutting plane method tangent sphere method protein flexibility protein dynamics of Biological Sciences, School of Life Sciences Rochester Institute of Technology One Lomb Memorial Drive, Rochester, NY 14623ĬP, cutting plane TS, tangent sphere CPM, cutting plane method TSM, tangent sphere method CPi, CP or CPM index TSi, TS or TSM index BS, binding site LBS, ligand BS GC, global or molecular centroid LC, local centroid PDB, Protein Data Bank of Pharmacology, School of Medicine, University of California, San Diego 9500 Gilman Drive, La Jolla, CA 92093-0636 & Dept. Reyes, Ph.D.* E-mail: *work done at:ĭept. The fourth, fifth and sixth programs determine the number of protein atoms lying on the negative side, positive side, and on the CP.ġ1 Implementation of the Tangent Sphere and Cutting Plane Methods in the Quantitative Determination of Ligand Binding Site Burial Depths in Proteins Using FORTRAN 77/90 Language The third determines the four coefficients A, B, C and D of the equation of the CP, Ax + By + Cz + D = 0. The second program finds the number of protein atoms inside, outside and on the TS. Its radius is the distance between the GC and the local centroid (LC), the centroid of the bound ligand or a portion of its binding site. The first program calculates the x-, y- and z-coordinates of the molecular geometric centroid of the protein (global centroid, GC), the center of the TS. The six FORTRAN programs we present here are: find_molec_centr.f, tangent_sphere.f, find_CP_coeffs.f, CPM_Neg_Side.f, CPM_Pos_Side.f and CPM_Zero_Side.f.

schaum outline of programming with fortran 77 pdf viewer

1996) are inagreement with their findings regarding cavity sizes in these proteins. We also show that results of the implementation of the TS and CP methods on six protein receptors (Laskowski et al. Particularly, we show here that application of the TS and CP methods on a theoretical model protein in the form of a spherical grid of points accurately portrays the behavior of the TS and CP indices, the predictive parameters obtained from the two methods. In this report, we present results that demonstrate the effectiveness of a set of FORTRAN 77 and 90 source codes used in the implementation of the two related procedures, as well as the precise implementation of the procedures. 2015a), we report on the Tangent Sphere (TS) and Cutting Plane (CP) methods - complementary methods to quantify, independent of protein size, the degree of ligand burial in a protein receptor. Ligand burial depth is an indicator of protein flexibility, as the extent of receptor conformational change required to bind a ligand in general varies directly with its depth of burial.








Schaum outline of programming with fortran 77 pdf viewer