Sentence examples for bonds were calculated using from inspiring English sources
3) Secondary structure attribution of residues and hydrogen bonds were calculated using DSSP [31].
Hydrogen bonds were calculated using HBOND routine available from the JOY package.
All residue-residue bonds were calculated using Pymol software [ 56] and all of the structures were visualized using the same software.
A detailed analysis of the interatomic contacts, interface complimentarity for each ligand-protein complex and a putative list of hydrogen bonds was calculated using the LPC/CSU software (Tables 2 and 3, Supporting Information File S1) [22].
The hydrophobic interactions and H-bonds were calculated using Ligplot program [ 39] where H-bonds were defined as acceptor-donor atom distances of less than 3.3 Å, hydrogen-acceptor atom distance of maximum 2.7 Å and acceptor-H-donor angle greater than 90°.
Number of distinct hydrogen bonds formed by specific residues to other amino acids within the protein during the simulation (NH bond) was calculated using g_hbond.
Bond lengths and bond angles were calculated using refined lattice parameters and fractional coordinates with the help of Powder Cell programme.
The rate constants for reactions involving bond formation or bond scission were calculated using transition state theory; collision theory was employed to calculate the rate constants for the adsorption desorption steps.
Generalized order parameters for NH bonds (S) were calculated using a method that accounts for the effects of rare conformational transitions on the bond vector orientation autocorrelation functions, described by Palmer and co-workers, from independent 4-ns trajectory slices.
Various simple physicochemical properties including molecular weight (Mwt), a log P, log D, polar surface area (PSA), H-bond donors and H-bond acceptors were calculated using the standard components in Pipeline Pilot.
