PocketAlign A Novel Algorithm for Aligning Binding Sites in Protein Structures

A fundamental task in bioinformatics involves a transfer of knowledge from one protein molecule onto another by way of recognizing similarities. Such similarities are obtained at different levels, that of sequence, whole fold, or important substructures. Comparison of binding sites is important to understand functional similarities among the proteins and also to understand drug cross-reactivities. Current methods in literature have their own merits and demerits, warranting exploration of newer concepts and algorithms, especially for large-scale comparisons and for obtaining accurate residue-wise mappings. Here, we report the development of a new algorithm, PocketAlign, for obtaining structural superpositions of binding sites. The software is available as a web-service at http://proline.physicslisc.emetin/pocketalign/. The algorithm encodes shape descriptors in the form of geometric perspectives, supplemented by chemical group classification. The shape descriptor considers several perspectives with each residue as the focus and captures relative distribution of residues around it in a given site. Residue-wise pairings are computed by comparing the set of perspectives of the first site with that of the second, followed by a greedy approach that incrementally combines residue pairings into a mapping. The mappings in different frames are then evaluated by different metrics encoding the extent of alignment of individual geometric perspectives. Different initial seed alignments are computed, each subsequently extended by detecting consequential atomic alignments in a three-dimensional grid, and the best 500 stored in a database. Alignments are then ranked, and the top scoring alignments reported, which are then streamed into Pymol for visualization and analyses. The method is validated for accuracy and sensitivity and benchmarked against existing methods. An advantage of PocketAlign, as compared to some of the existing tools available for binding site comparison in literature, is that it explores different schemes for identifying an alignment thus has a better potential to capture similarities in ligand recognition abilities. PocketAlign, by finding a detailed alignment of a pair of sites, provides insights as to why two sites are similar and which set of residues and atoms contribute to the similarity.

Efficient syntheses of benzothiazepines as antagonists for the mitochondrial sodium-calcium exchanger: Potential therapeutics for type II diabetes

Type II diabetes mellitus is a chronic metabolic disorder that can lead to serious cardiovascular, renal, neurologic, and retinal complications. While several drugs are currently prescribed to treat type II diabetes, their efficacy is limited by mechanism-related side effects (weight gain, hypoglycemia, gastrointestinal distress), inadequate efficacy for use as monotherapy, and the development of tolerance to the agents. Consequently, combination therapies are frequently employed to effectively regulate blood glucose levels. We have focused on the mitochondrial sodium-calcium exchanger (mNCE) as a novel target for diabetes drug discovery. We have proposed that inhibition of the mNCE can be used to regulate calcium flux across the mitochondrial membrane, thereby enhancing mitochondrial oxidative metabolism, which in turn enhances glucose-stimulated insulin secretion (GSIS) in the pancreatic beta-cell. In this paper, we report the facile synthesis of benzothiazepines and derivatives by S-alkylation using 2-aminobenzhydrols. The syntheses of other bicyclic analogues based on benzothiazepine, benzothiazecine, benzodiazecine, and benzodiazepine templates are also described. These compounds have been evaluated for their inhibition of mNCE activity, and the results from the structure-activity relationship (SAR) studies are discussed.

Investigation on the Potential Rise and Currents in Insulated Mast Scheme with Single Tower During Stroke Interception

The insulated mast scheme for the lightning protection system can be found in a few practical designs. Many advantages over conventional protection system are some times envisaged. However, the technical literature on the analysis of such schemes and further quantification of their protection efficacy is rather scarce. As a first step to address this problem, the present work is taken up and the potential rise at the top and ground end currents in insulating mast scheme with single tower is investigated for several tower heights and pertinent values of other parameters. The quantities that are investigated are the potential difference across the insulation and ground end currents for both tower and the ground wires. Quantifications are carried out for the relevant range of stroke current front times. The influence of number of ground wires, their earthing location and to a limited extent, the length of the insulating support have been ascertained. Some relevant discussion on insulation strength is made. These findings are quite novel and aid in quantification of the practical efficacy of the insulated mast scheme. The level of induction to the support tower and possible flashover to the same are not in favour of this scheme.

Hotspots of solar potential in India

Solar hotspots are the regions characterized by an exceptional solar power potential suitable for decentralized commercial exploitation of energy. Identification of solar hotspots in a vast geographical expanse with dense habitations helps to meet escalating power demand in a decentralized, efficient and sustainable manner. This communication focuses on the assessment of resource potential with variability in India derived from high resolution satellite derived insolation data. Data analysis reveals that nearly 58% of the geographical area potentially represent the solar hotspots in the country with more than 5 kWh/m(2)/day of annual average Global insolation. A techno-economic analysis of the solar power technologies and a prospective minimal utilization of the land available within these solar hotspots demonstrate their immense power generation as well as emission reduction potential. The study evaluates the progress made in solar power generation in the country especially with the inception of an ambitious National Solar Mission (NSM) also termed as `Solar India'. The organizational aspects of solar power generation with focus on existing policy elements are also addressed so as to probe the actual potential of the identified solar hotspots in meeting the NSM targets and beyond. (C) 2011 Elsevier Ltd. All rights reserved.

Potential and Electric Field Profiles for Transmission line Insulators

Transmission of bulk power at high voltages over very long distances has become very imperative. At present, throughout the globe, this task has been mostly performed by overhead transmission lines. The dual task of mechanically supporting and electrically isolating the live phase conductors from the support tower is performed by string insulators. Whether in clean condition or under polluted conditions, the electrical stress distribution along the insulators governs the possible flashover, which is quite detrimental to the system. However, a reliable data on stress distribution in commonly employed string insulators are rather scarce. Considering this, the present work has made an attempt to study accurately, the field distribution in 220 kV strings for six different types of porcelain/ceramic insulators (Normal and Antifog discs) used for high voltage transmission. The surface charge simulation method is employed for the required field computation. Voltage and electric stress distribution is deduced and compared across different types of discs. A comparison on normalised surface resistance, which is an indicator for the stress concentration under polluted condition, is also attempted.

Network Rhythms Influence the Relationship between Spike-Triggered Local Field Potential and Functional Connectivity

Characterizing the functional connectivity between neurons is key for understanding brain function. We recorded spikes and local field potentials (LFPs) from multielectrode arrays implanted in monkey visual cortex to test the hypotheses that spikes generated outward-traveling LFP waves and the strength of functional connectivity depended on stimulus contrast, as described recently. These hypotheses were proposed based on the observation that the latency of the peak negativity of the spike-triggered LFP average (STA) increased with distance between the spike and LFP electrodes, and the magnitude of the STA negativity and the distance over which it was observed decreased with increasing stimulus contrast. Detailed analysis of the shape of the STA, however, revealed contributions from two distinct sources-a transient negativity in the LFP locked to the spike (similar to 0 ms) that attenuated rapidly with distance, and a low-frequency rhythm with peak negativity similar to 25 ms after the spike that attenuated slowly with distance. The overall negative peak of the LFP, which combined both these components, shifted from similar to 0 to similar to 25 ms going from electrodes near the spike to electrodes far from the spike, giving an impression of a traveling wave, although the shift was fully explained by changing contributions from the two fixed components. The low-frequency rhythm was attenuated during stimulus presentations, decreasing the overall magnitude of the STA. These results highlight the importance of accounting for the network activity while using STAs to determine functional connectivity.

WEPA: Wind energy potential assessment-spatial decision support system

Spatial Decision Support System (SDSS) assist in strategic decision-making activities considering spatial and temporal variables, which help in Regional planning. WEPA is a SDSS designed for assessment of wind potential spatially. A wind energy system transforms the kinetic energy of the wind into mechanical or electrical energy that can be harnessed for practical use. Wind energy can diversify the economies of rural communities, adding to the tax base and providing new types of income. Wind turbines can add a new source of property value in rural areas that have a hard time attracting new industry. Wind speed is extremely important parameter for assessing the amount of energy a wind turbine can convert to electricity: The energy content of the wind varies with the cube (the third power) of the average wind speed. Estimation of the wind power potential for a site is the most important requirement for selecting a site for the installation of a wind electric generator and evaluating projects in economic terms. It is based on data of the wind frequency distribution at the site, which are collected from a meteorological mast consisting of wind anemometer and a wind vane and spatial parameters (like area available for setting up wind farm, landscape, etc.). The wind resource is governed by the climatology of the region concerned and has large variability with reference to space (spatial expanse) and time (season) at any fixed location. Hence the need to conduct wind resource surveys and spatial analysis constitute vital components in programs for exploiting wind energy. SDSS for assessing wind potential of a region / location is designed with user friendly GUI’s (Graphic User Interface) using VB as front end with MS Access database (backend). Validation and pilot testing of WEPA SDSS has been done with the data collected for 45 locations in Karnataka based on primary data at selected locations and data collected from the meteorological observatories of the India Meteorological Department (IMD). Wind energy and its characteristics have been analysed for these locations to generate user-friendly reports and spatial maps. Energy Pattern Factor (EPF) and Power Densities are computed for sites with hourly wind data. With the knowledge of EPF and mean wind speed, mean power density is computed for the locations with only monthly data. Wind energy conversion systems would be most effective in these locations during May to August. The analyses show that coastal and dry arid zones in Karnataka have good wind potential, which if exploited would help local industries, coconut and areca plantations, and agriculture. Pre-monsoon availability of wind energy would help in irrigating these orchards, making wind energy a desirable alternative.

Solar energy potential assessment using GIS

Renewable energy resources are those having a cycling time less than 100 years and are renewed by the nature and their supply exceeds the rate of consumption. Renewable energy systems use resources that are constantly replaced in nature and are usually less polluting. In order to tap the potential of renewable energy sources, there is a need to assess the availability of resources spatially as well as temporally. Geographic Information Systems (GIS) along with Remote Sensing (RS) helps in mapping on spatial and temporal scales of the resources and demand. The spatial database of resource availability and the demand would help in the regional energy planning. This paper discusses the application of geographical information system (GIS) to map the solar potential in Karnataka state, India. Regions suitable for tapping solar energy are mapped on the basis of global solar radiation data, and this analysis provides a picture of the potential. The study identifies that Coastal parts of Karnataka with the higher global solar radiation is ideally suited for harvesting solar energy. The potential analysis reveals that, maximum global solar radiation is in districts such as Uttara Kannada and Dakshina Kannada. Global solar radiation in Uttara Kannada during summer, monsoon and winter are 6.31, 4.40 and 5.48 kWh/sq.m, respectively. Similarly, Dakshina Kannada has 6.16, 3.89 and 5.21 kWh/sq.m during summer, monsoon and winter.

Geographical Information System Approach for Regional Biogas Potential Assessment

The economic prosperity and quality of life in a region are closely linked to the level of its per capita energy consumption. In India more than 70% of the total population inhabits rural areas and 85-90% of energy requirement is being met by bioresources. With dwindling resources, attention of planners is diverted to viable energy alternatives to meet the rural energy demand. Biogas as fuel is one such alternative, which can be obtained by anaerobic digestion of animal residues and domestic and farm wastes, abundantly available in the countryside. Study presents the techniques to assess biogas potential spatially using GIS in Kolar district, Karnataka State, India. This would help decision makers in selecting villages for implementing biogas programmes based on resource availability. Analyses reveal that the domestic energy requirement of more than 60% population can be met by biogas option. This is based on the estimation of the per capita requirement of gas for domestic purposes and availability of livestock residues.

Mesoscopics nanoscopics and macroscopics materials

At the present time, materials with dimensions in the range of microns to nanometers have become the prime objects of vigorous research activities of all over the world. The possibility of artificially creating novel materials with exotic and tailor made properties that are essential for future development in the frontier areas of electronics, photonics, spintronics etc has generated much interest in the study of these mesoscopic and nanoscopic materials. These materials also have the potential for wide ranging economically viable technological, industrial, engineering and bio-medical applications. They may consist of metals , alloys , ceramics, polymers, composites and biological materials; which are usually assembled at the atomic / molecular level to achieve new properties. Understanding the underlying science and characterization of these new materials with a view of harnessing their exotic properties is the prime focus of the researchers. These Proceedings address these issues relating to mesoscopic, nanoscopic and macroscopic materials.

Exploring the spectral enantiodiscrimination potential of a DNA-based orienting medium using deuterium NMR spectroscopy

(2)H-{(1)H} 1D and 2D-NMR spectroscopy is used to evaluate the enantiodiscrimination potential of DNA-based, lyotropic chiral mesophases on a series of (pro) chiral amino acids.