Online_DPI: a web server to calculate the diffraction precision index for a protein structure

An online computing server, Online_DPI (where DPI denotes the diffraction precision index), has been created to calculate the `Cruickshank DPI' value for a given three-dimensional protein or macromolecular structure. It also estimates the atomic coordinate error for all the atoms available in the structure. It is an easy-to-use web server that enables users to visualize the computed values dynamically on the client machine. Users can provide the Protein Data Bank (PDB) identification code or upload the three-dimensional atomic coordinates from the client machine. The computed DPI value for the structure and the atomic coordinate errors for all the atoms are included in the revised PDB file. Further, users can graphically view the atomic coordinate error along with `temperature factors' (i.e. atomic displacement parameters). In addition, the computing engine is interfaced with an up-to-date local copy of the Protein Data Bank. New entries are updated every week, and thus users can access all the structures available in the Protein Data Bank. The computing engine is freely accessible online at http://cluster.physics.iisc.ernet.in/dpi/.

Three-dimensional warping in strip-based composite four-bar mechanisms

This work intends to demonstrate the effect of geometrically non-linear cross-sectional analysis of certain composite beam-based four-bar mechanisms in predicting the three-dimensional warping of the cross-section. The only restriction in the present analysis is that the strains within each elastic body remain small (i.e., this work does not deal with materials exhibiting non-linear constitutive laws at the 3-D level). Here, all component bars of the mechanism are made of fiber-reinforced laminates. They could, in general, be pre-twisted and/or possess initial curvature, either by design or by defect. Each component of the mechanism is modeled as a beam based on geometrically non-linear 3-D elasticity theory. The component problems are thus split into 2-D analyses of reference beam cross-sections and non-linear 1-D analyses along the three beam reference curves. The splitting of the three-dimensional beam problem into two- and one-dimensional parts, called dimensional reduction, results in a tremendous savings of computational effort relative to the cost of three-dimensional finite element analysis, the only alternative for realistic beams. The analysis of beam-like structures made of laminated composite materials requires a much more complicated methodology. Hence, the analysis procedure based on Variational Asymptotic Method (VAM), a tool to carry out the dimensional reduction, is used here. The representative cross-sections of all component bars are analyzed using two different approaches: (1) Numerical Model and (2) Analytical Model. Four-bar mechanisms are analyzed using the above two approaches for Omega = 20 rad/s and Omega = pi rad/s and observed the same behavior in both cases. The noticeable snap-shots of the deformation shapes of the mechanism about 1000 frames are also reported using commercial software (I-DEAS + NASTRAN + ADAMS). The maximum out-of-plane warping of the cross-section is observed at the mid-span of bar-1, bar-2 and bar-3 are 1.5 mm, 250 mm and 1.0 mm, respectively, for t = 0:5 s. (C) 2015 Elsevier Ltd. All rights reserved.

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

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/.