Computer-Aided Drug Design of Pyranopyrazoles and Related Compounds for Checkpoint Kinase-1

Checkpoint-1 kinase plays an important role in the G(2)M cell cycle control, therefore its inhibition by small molecules is of great therapeutic interest in oncology. In this paper, we have reported the virtual screening of an in-house library of 2499 pyranopyrazole derivatives against the ATP-binding site of Chk1 kinase using Glide 5.0 program, which resulted in six hits. All these ligands were docked into the site forming most crucial interactions with Cys87, Glu91 and Leu15 residues. From the observed results these ligands are suggested to be potent inhibitors of Chk1 kinase with sufficient scope for further elaboration.

NUVIEW:software for display and interactive manipulation of nucleic acid models

The NUVIEW software package allows skeletal models of any double helical nucleic acid molecule to be displayed out a graphics monitor and to apply various rotations, translations and scaling transformations interactively, through the keyboard. The skeletal model is generated by connecting any pair of representative points, one from each of the bases in the basepair. In addition to the above mentioned manipulations, the base residues can be identified by using a locator and the distance between any pair of residues can be obtained. A sequence based color coded display allows easy identification of sequence repeats, such as runs of Adenines. The real time interactive manipulation of such skeletal models for large DNA/RNA double helices, can be used to trace the path of the nucleic acid chain in three dimensions and hence get a better idea of its topology, location of linear or curved regions, distances between far off regions in the sequence etc. A physical picture of these features will assist in understanding the relationship between base sequence, structure and biological function in nucleic acids.

Learning Feature Trajectories Using Gabor Filter Bank for Human Activity Segmentation and Recognition

We describe a novel method for human activity segmentation and interpretation in surveillance applications based on Gabor filter-bank features. A complex human activity is modeled as a sequence of elementary human actions like walking, running, jogging, boxing, hand-waving etc. Since human silhouette can be modeled by a set of rectangles, the elementary human actions can be modeled as a sequence of a set of rectangles with different orientations and scales. The activity segmentation is based on Gabor filter-bank features and normalized spectral clustering. The feature trajectories of an action category are learnt from training example videos using dynamic time warping. The combined segmentation and the recognition processes are very efficient as both the algorithms share the same framework and Gabor features computed for the former can be used for the later. We have also proposed a simple shadow detection technique to extract good silhouette which is necessary for good accuracy of an action recognition technique.

Software Pipelined Execution of Stream Programs on GPUs

The StreamIt programming model has been proposed to exploit parallelism in streaming applications on general purpose multi-core architectures. This model allows programmers to specify the structure of a program as a set of filters that act upon data, and a set of communication channels between them. The StreamIt graphs describe task, data and pipeline parallelism which can be exploited on modern Graphics Processing Units (GPUs), as they support abundant parallelism in hardware. In this paper, we describe the challenges in mapping StreamIt to GPUs and propose an efficient technique to software pipeline the execution of stream programs on GPUs. We formulate this problem - both scheduling and assignment of filters to processors - as an efficient Integer Linear Program (ILP), which is then solved using ILP solvers. We also describe a novel buffer layout technique for GPUs which facilitates exploiting the high memory bandwidth available in GPUs. The proposed scheduling utilizes both the scalar units in GPU, to exploit data parallelism, and multiprocessors, to exploit task and pipelin parallelism. Further it takes into consideration the synchronization and bandwidth limitations of GPUs, and yields speedups between 1.87X and 36.83X over a single threaded CPU.

A hybrid computer for X-ray crystallography

A hybrid computer for structure factor calculations in X-ray crystallography is described. The computer can calculate three-dimensional structure factors of up to 24 atoms in a single run and can generate the scatter functions of well over 100 atoms using Vand et al., or Forsyth and Wells approximations. The computer is essentially a digital computer with analog function generators, thus combining to advantage the economic data storage of digital systems and simple computing circuitry of analog systems. The digital part serially selects the data, computes and feeds the arguments into specially developed high precision digital-analog function generators, the outputs of which being d.c. voltages, are further processed by analog circuits and finally the sequential adder, which employs a novel digital voltmeter circuit, converts them back into digital form and accumulates them in a dekatron counter which displays the final result. The computer is also capable of carrying out 1-, 2-, or 3-dimensional Fourier summation, although in this case, the lack of sufficient storage space for the large number of coefficients involved, is a serious limitation at present.

GAP-RBF based NR image quality measurement for JPEG coded images

In this paper, we present a growing and pruning radial basis function based no-reference (NR) image quality model for JPEG-coded images. The quality of the images are estimated without referring to their original images. The features for predicting the perceived image quality are extracted by considering key human visual sensitivity factors such as edge amplitude, edge length, background activity and background luminance. Image quality estimation involves computation of functional relationship between HVS features and subjective test scores. Here, the problem of quality estimation is transformed to a function approximation problem and solved using GAP-RBF network. GAP-RBF network uses sequential learning algorithm to approximate the functional relationship. The computational complexity and memory requirement are less in GAP-RBF algorithm compared to other batch learning algorithms. Also, the GAP-RBF algorithm finds a compact image quality model and does not require retraining when the new image samples are presented. Experimental results prove that the GAP-RBF image quality model does emulate the mean opinion score (MOS). The subjective test results of the proposed metric are compared with JPEG no-reference image quality index as well as full-reference structural similarity image quality index and it is observed to outperform both.

Text localization and extraction from complex gray images

We propose two texture-based approaches, one involving Gabor filters and the other employing log-polar wavelets, for separating text from non-text elements in a document image. Both the proposed algorithms compute local energy at some information-rich points, which are marked by Harris' corner detector. The advantage of this approach is that the algorithm calculates the local energy at selected points and not throughout the image, thus saving a lot of computational time. The algorithm has been tested on a large set of scanned text pages and the results have been seen to be better than the results from the existing algorithms. Among the proposed schemes, the Gabor filter based scheme marginally outperforms the wavelet based scheme.

Computer modelling approach to study the modes of binding of alpha- and beta-anomers of D-galactose, D-fucose and D-glucose to L-arabinose-binding protein

The modes of binding of alpha- and beta-anomers of D-galactose, D-fucose and D-glucose to L-arabinose-binding protein (ABP) have been studied by energy minimization using the low resolution (2.4 A) X-ray data of the protein. These studies suggest that these sugars preferentially bind in the alpha-form to ABP, unlike L-arabinose where both alpha- and beta-anomers bind almost equally. The best modes of binding of alpha- and beta-anomers of D-galactose and D-fucose differ slightly in the nature of the possible hydrogen bonds with the protein. The residues Arg 151 and Asn 232 of ABP from bidentate hydrogen bonds with both L-arabinose and D-galactose, but not with D-fucose or D-glucose. However in the case of L-arabinose, Arg 151 forms hydrogen bonds with the hydroxyl group at the C-4 atom and the ring oxygen, whereas in case of D-galactose it forms bonds with the hydroxyl groups at the C-4 and C-6 atoms of the pyranose ring. The calculated conformational energies also predict that D-galactose is a better inhibitor than D-fucose and D-glucose, in agreement with kinetic studies. The weak inhibitor D-glucose binds preferentially to one domain of ABP leading to the formation of a weaker complex. Thus these studies provide information about the most probable binding modes of these sugars and also provide a theoretical explanation for the observed differences in their binding affinities.

Computer simulation of protein—carbohydrate complexes: application to arabinose-binding protein and pea lectin

The CCEM method (Contact Criteria and Energy Minimisation) has been developed and applied to study protein-carbohydrate interactions. The method uses available X-ray data even on the native protein at low resolution (above 2.4 Å) to generate realistic models of a variety of proteins with various ligands.The two examples discussed in this paper are arabinose-binding protein (ABP) and pea lectin. The X-ray crystal structure data reported on ABP-β-l-arabinose complex at 2.8, 2.4 and 1.7 Å resolution differ drastically in predicting the nature of the interactions between the protein and ligand. It is shown that, using the data at 2.4 Å resolution, the CCEM method generates complexes which are as good as the higher (1.7 Å) resolution data. The CCEM method predicts some of the important hydrogen bonds between the ligand and the protein which are missing in the interpretation of the X-ray data at 2.4 Å resolution. The theoretically predicted hydrogen bonds are in good agreement with those reported at 1.7 Å resolution. Pea lectin has been solved only in the native form at 3 Å resolution. Application of the CCEM method also enables us to generate complexes of pea lectin with methyl-α-d-glucopyranoside and methyl-2,3-dimethyl-α-d-glucopyranoside which explain well the available experimental data in solution.

Design and performance evaluation of a systolic architecture for hidden-surface removal

In this paper, we propose a systolic architecture for hidden-surface removal. Systolic architecture is a kind of parallel architecture best known for its easy VLSI implementability. After discussing the design details of the architecture, we present the results of the simulation experiments conducted in order to evaluate the performance of the architecture.

A computer study of the miscibility limits of Pd-Cu-Si

Metallic glasses are of interest because of their mechanical properties. They are ductile as well as brittle. This is true of Pd77.5Cu6Si16.5, a ternary glassy alloy. Actually, the most stable metallic glasses are those which are alloys of noble or transition metals A general formula is postulated as T70–80G30-20where T stands for one or several 3d transition elements, and includes the metalloid glass formers. Another general formula is A3B to A5B where B is a metalloid. A computer method utilising the MIGAP computer program of Kaufman is used to calculate the miscibility gap over a range of temperatures. The precipitation of a secondary crystalline phase is postulated around 1500K. This could produce a dispersed phase composite with interesting high temperature-strength properties.

A computer study of the miscibility limits of Sb-Te-Bi

The quaternary system Sb1bTe1bBi1bSe with small amounts of suitable dopants is of interest for the manufacture of thermoelectric modules which exhibit the Peltier and Seebeck effects. This property could be useful in the production of energy from the thermoelectric effect. Other substances are bismuth telluride (Bi2Te3) and Sb1bTe1bBi and compounds such as ZnIn2Se4. In the present paper the application of computer programs such as MIGAP of Kaufman is used to indicate the stability of the ternary limits of Sb1bTe1bBi within the temperature ranges of interest, namely 273 K to 300 K.

Computer estimation of the Cd---Hg---Te phase diagram

The compounds CdHgTe and its constituent binaries CdTe, HgTe, and CdHg are semiconductors which are used in thermal, infrared, nuclear, thermoelectric and other photo sensitive devices. The compound CdHgTe has a Sphaleritic structure of possible type A1IIB1IIC6VI. The TERCP program of Kaufman is used to estimate the stable regions of the ternary phase diagram using available thermodynamic data. It was found that there was little variation in stochiometry with temperature. The compositions were calculated for temperatures ranging from 325K to 100K and the compositional limits were Cd13−20Hg12−01Te75−79, Hg varying most. By comparison with a similar compound, Cd In2Te4 of forbidden band width. 88 to .90 e.V., similar properties are postulated for Cd1Hg1Te6 with applications in the infra red region of the spectrum at 300K where this composition is given by TERCP at the limit of stability.