Hydrogen Bonds Computing Server (HBCS): an online web server to compute hydrogen-bond interactions and their precision

Abstract

Hydrogen bonds in biological macromolecules play significant structural and functional roles. They are the key contributors to most of the interactions without which no living system exists. In view of this, a web-based computing server, the Hydrogen Bonds Computing Server (HBCS), has been developed to compute hydrogen-bond interactions and their standard deviations for any given macromolecular structure. The computing server is connected to a locally maintained Protein Data Bank (PDB) archive. Thus, the user can calculate the above parameters for any deposited structure, and options have also been provided for the user to upload a structure in PDB format from the client machine. In addition, the server has been interfaced with the molecular viewers Jmol and JSmol to visualize the hydrogen-bond interactions. The proposed server is freely available and accessible via the World Wide Web at http:// bioserver1.physics.iisc.ernet.in/hbcs/.

A Geometric Definition of Short to Medium Range Hydrogen-Mediated Interactions in Proteins

“…Because this method is more general than those that specifically investigated these interactions (possibly due to their relative rarity [41]), our inability to detect aromatic π-interactions in no way disproves their existence [13,21,58]. Nor should these results in anyway detract from the power of the many widely used methods that deal with hydrogen placement in proteins which have long stood the test of time [9,39,52,53]. Rather, we propose this model as a way to extend the functionalities of those gold-standard methods.…”

“…It should be noted that removing the hydrogen atom from the place of central importance and the somewhat arbitrary decisions used to choose the angular limits [21,43], as well as our somewhat unusual inclusion of hydrogens with free rotations [24], makes it difficult to compare interaction angles between this analysis of HMIs with other protein hydrogen bond analyses [2,4,7,[52][53][54]. However, we note that we found no donor-centered interactions longer than the common distance limit of 3.5 Å [2,4,20,25,55,56] and only one acceptor interaction ( Table 1) greater than that length despite measuring interactions out to 6 Å.…”

NIMS: a database on nucleobase compounds and their interactions in macromolecular structures

“…This database also reports the diffraction precision index (DPI) (Gurusaran et al, 2014;Cruickshank, 1999) of the protein structure, calculated using the Online_DPI server (Kumar et al, 2015), as well as the calculated 'atomic uncertainty' (Gurusaran et al, 2014) values for each atom in the protein structure. Further, the standard deviations (errors) of interatomic distances and angles calculated from the atomic uncertainty values are displayed alongside the interaction distances and angles (Gurusaran et al, 2016). Hydrogen atoms were added using the program REDUCE (Word et al, 1999) and are displayed in the PDB file under a separate option to view 'hydrogen added file', with the inclusion of the atomic uncertainty values.…”

MRPC (Missing Regions in Polypeptide Chains): a knowledgebase

“…X-ray crystallography has for many years been the paramount technique for determining the three-dimensional structure of proteins (Praveen et al, 2008;Berman et al, 2014). In X-ray crystallographic experiments, and thus in many of the three-dimensional structures deposited in the PDB, the loops and ends of the polypeptide chains and certain residues in the middle portion of the chain are not observed owing to poor electron density (Sumathi et al, 2006;Saravanan et al, 2010;Djinovic Carugo & Carugo, 2015;Gurusaran et al, 2016). Thus, these regions will not be available in the atomic coordinates file submitted to the PDB and they are referred to as 'missing regions' (Ananthalakshmi, Kumar et al, 2005;Ananthalakshmi, Samayamohan et al, 2005;Nagarajan et al, 2012;Santhosh et al, 2019).…”