CSSP (Consensus Secondary Structure Prediction): a web-based server for structural biologists

Sequence-structure correlation studies are important in deciphering the relationships between various structural aspects, which may shed light on the protein-folding problem. The first step of this process is the prediction of secondary structure for a protein sequence of unknown three-dimensional structure. To this end, a web server has been created to predict the consensus secondary structure using well known algorithms from the literature. Furthermore, the server allows users to see the occurrence of predicted secondary structural elements in other structure and sequence databases and to visualize predicted helices as a helical wheel plot. The web server is accessible at http://bioserver1.physics.iisc.ernet.in/cssp/.

On vibration of eccentrically stiffened plates with varying stiffener length

Results of a study of the variation of natural frequencies with respect to the length of the stiffener of a square panel clamped all along its boundary and stiffened in the middle by a concentric stiffener were recently reported [ 11. Significant increases in certain frequencies, namely those with modes symmetric about both the medians of the plate, were observed when small gaps were not left between the plate boundary and the stiffener end. As an extension to that work, results of a study of the effect of the eccentricity of the stiffener on the frequency variation with the length of the stiffener are reported here.

BSDD-2.0: Biomolecules Segment Display Device - An updated web accessible computing resource

The existing internet computing resource, Biomolecules Segment Display Device (BSDD), has been updated with several additional useful features. An advanced option is provided to superpose the structural motifs obtained from a search on the Protein Data Bank (PDB) in order to see if the three-dimensional structures adopted by identical or similar sequence motifs are the same. Furthermore, the options to display structural aspects like inter- and intra-molecular interactions, ion-pairs, disulphide bonds, etc. have been provided.The updated resource is interfaced with an up-to-date copy of the public domain PDB as well as 25 and 90% non-redundant protein structures. Further, users can upload the three-dimensional atomic coordinates (PDB format) from the client machine. A free molecular graphics program, JMol, is interfaced with it to display the three-dimensional structures.

Finite element analysis of bimodulus composite stiffened thin shells of revolution

This paper is a sequel to the work published by the first and third authors[l] on stiffened laminated shells of revolution made of unimodular materials (materials having identical properties in tension and compression). A finite element analysis of laminated bimodulus composite thin shells of revolution, reinforced by laminated bimodulus composite stiffeners is reported herein. A 48 dot doubly curved quadrilateral laminated anisotropic shell of revolution finite element and it's two compatible 16 dof stiffener finite elements namely: (i) a laminated anisotropic parallel circle stiffener element (PCSE) and (ii) a laminated anisotropic meridional stiffener element (MSE) have been used iteratively. The constitutive relationship of each layer is assumed to depend on whether the fiberdirection strain is tensile or compressive. The true state of strain or stress is realized when the locations of the neutral surfaces in the shell and the stiffeners remain unaltered (to a specified accuracy) between two successive iterations. The solutions for static loading of a stiffened plate, a stiffened cylindrical shell. and a stiffened spherical shell, all made of bimodulus composite materials, have been presented.

An Optimal Mechanism for Sponsored Search Auctions on the Web and Comparison With Other Mechanisms

In this paper, we first describe a framework to model the sponsored search auction on the web as a mechanism design problem. Using this framework, we describe two well-known mechanisms for sponsored search auction-Generalized Second Price (GSP) and Vickrey-Clarke-Groves (VCG). We then derive a new mechanism for sponsored search auction which we call optimal (OPT) mechanism. The OPT mechanism maximizes the search engine's expected revenue, while achieving Bayesian incentive compatibility and individual rationality of the advertisers. We then undertake a detailed comparative study of the mechanisms GSP, VCG, and OPT. We compute and compare the expected revenue earned by the search engine under the three mechanisms when the advertisers are symmetric and some special conditions are satisfied. We also compare the three mechanisms in terms of incentive compatibility, individual rationality, and computational complexity. Note to Practitioners-The advertiser-supported web site is one of the successful business models in the emerging web landscape. When an Internet user enters a keyword (i.e., a search phrase) into a search engine, the user gets back a page with results, containing the links most relevant to the query and also sponsored links, (also called paid advertisement links). When a sponsored link is clicked, the user is directed to the corresponding advertiser's web page. The advertiser pays the search engine in some appropriate manner for sending the user to its web page. Against every search performed by any user on any keyword, the search engine faces the problem of matching a set of advertisers to the sponsored slots. In addition, the search engine also needs to decide on a price to be charged to each advertiser. Due to increasing demands for Internet advertising space, most search engines currently use auction mechanisms for this purpose. These are called sponsored search auctions. A significant percentage of the revenue of Internet giants such as Google, Yahoo!, MSN, etc., comes from sponsored search auctions. In this paper, we study two auction mechanisms, GSP and VCG, which are quite popular in the sponsored auction context, and pursue the objective of designing a mechanism that is superior to these two mechanisms. In particular, we propose a new mechanism which we call the OPT mechanism. This mechanism maximizes the search engine's expected revenue subject to achieving Bayesian incentive compatibility and individual rationality. Bayesian incentive compatibility guarantees that it is optimal for each advertiser to bid his/her true value provided that all other agents also bid their respective true values. Individual rationality ensures that the agents participate voluntarily in the auction since they are assured of gaining a non-negative payoff by doing so.

SSMBS: a web server to locate sequentially separated motifs in biological sequences

The identification of sequence (amino acids or nucleotides) motifs in a particular order in biological sequences has proved to be of interest. This paper describes a computing server, SSMBS, which can locate anddisplay the occurrences of user-defined biologically important sequence motifs (a maximum of five) present in a specific order in protein and nucleotide sequences. While the server can efficiently locate motifs specified using regular expressions, it can also find occurrences of long and complex motifs. The computation is carried out by an algorithm developed using the concepts of quantifiers in regular expressions. The web server is available to users around the clock at http://dicsoft1.physics.iisc.ernet.in/ssmbs/.

A combinatorial procurement auction for QoS-aware web services

Business processes and application functionality are becoming available as internal web services inside enterprise boundaries as well as becoming available as commercial web services from enterprise solution vendors and web services marketplaces. Typically there are multiple web service providers offering services capable of fulfilling a particular functionality, although with different Quality of Service (QoS). Dynamic creation of business processes requires composing an appropriate set of web services that best suit the current need. This paper presents a novel combinatorial auction approach to QoS aware dynamic web services composition. Such an approach would enable not only stand-alone web services but also composite web services to be a part of a business process. The combinatorial auction leads to an integer programming formulation for the web services composition problem. An important feature of the model is the incorporation of service level agreements. We describe a software tool QWESC for QoS-aware web services composition based on the proposed approach.

Fracture analysis of stiffened panels under combined tensile, bending, and shear loads

The objective is to present the formulation of numerically integrated modified virtual crack closure integral technique for concentrically and eccentrically stiffened panels for computation of strain-energy release rate and stress intensity factor based on linear elastic fracture mechanics principles. Fracture analysis of cracked stiffened panels under combined tensile, bending, and shear loads has been conducted by employing the stiffened plate/shell finite element model, MQL9S2. This model can be used to analyze plates with arbitrarily located concentric/eccentric stiffeners, without increasing the total number of degrees of freedom, of the plate element. Parametric studies on fracture analysis of stiffened plates under combined tensile and moment loads have been conducted. Based on the results of parametric,studies, polynomial curve fitting has been carried out to get best-fit equations corresponding to each of the stiffener positions. These equations can be used for computation of stress intensity factor for cracked stiffened plates subjected to tensile and moment loads for a given plate size, stiffener configuration, and stiffener position without conducting finite element analysis.

Determination of the orthotropic plate parameters of stiffened plates and grillages in free vibration

It is well known that the analysis of vibration of orthogonally stiffened rectangular plates and grillages may be simplified by replacing the actual structure by an orthotropic plate. This needs a suitable determination of the four elastic rigidity constants Dx, Dy, Dxy, D1 and the mass {Mathematical expression} of the orthotropic plate. A method is developed here for determining these parameters in terms of the sectional properties of the original plate-stiffener combination or the system of interconnected beams. Results of experimental work conducted on aluminium plates agree well with the results of the theory developed here.

Protein Block Expert (PBE): a web-based protein structure analysis server using a structural alphabet

Encoding protein 3D structures into 1D string using short structural prototypes or structural alphabets opens a new front for structure comparison and analysis. Using the well-documented 16 motifs of Protein Blocks (PBs) as structural alphabet, we have developed a methodology to compare protein structures that are encoded as sequences of PBs by aligning them using dynamic programming which uses a substitution matrix for PBs. This methodology is implemented in the applications available in Protein Block Expert (PBE) server. PBE addresses common issues in the field of protein structure analysis such as comparison of proteins structures and identification of protein structures in structural databanks that resemble a given structure. PBE-T provides facility to transform any PDB file into sequences of PBs. PBE-ALIGNc performs comparison of two protein structures based on the alignment of their corresponding PB sequences. PBE-ALIGNm is a facility for mining SCOP database for similar structures based on the alignment of PBs. Besides, PBE provides an interface to a database (PBE-SAdb) of preprocessed PB sequences from SCOP culled at 95% and of all-against-all pairwise PB alignments at family and superfamily levels. PBE server is freely available at http://bioinformatics.univ-reunion.fr/ PBE/.

Cascade PSI-BLAST web server: a remote homology search tool for relating protein domains

Owing to high evolutionary divergence, it is not always possible to identify distantly related protein domains by sequence search techniques. Intermediate sequences possess sequence features of more than one protein and facilitate detection of remotely related proteins. We have demonstrated recently the employment of Cascade PSI-BLAST where we perform PSI-BLAST for many 'generations', initiating searches from new homologues as well. Such a rigorous propagation through generations of PSI-BLAST employs effectively the role of intermediates in detecting distant similarities between proteins. This approach has been tested on a large number of folds and its performance in detecting superfamily level relationships is similar to 35% better than simple PSI-BLAST searches. We present a web server for this search method that permits users to perform Cascade PSI-BLAST searches against the Pfam, SCOP and SwissProt databases. The URL for this server is http://crick.mbu.iisc.ernet.in/similar to CASCADE/CascadeBlast.html.

Ultimate Strength of RC Wall Panels with Openings

Test results of 12 reinforced concrete (RC) wall panels with openings are presented. The panels have been subjected to in-plane vertical loads applied at an eccentricity to represent possible accidental eccentricity that occurs in practice due to constructional imperfections. The 12 specimens consist of two identical groups of six panels each. One group of panels is tested in one-way in-plane action (i.e., supported at top and bottom edges against lateral displacement). The second group of panels is tested in two-way in-plane action (i.e., supported on all the four edges against lateral displacement). Openings in the panels represent typical door and window openings. Cracking loads, ultimate loads, crack patterns, and lateral deflections of the panels are studied. Empirical methods have been developed for the prediction of ultimate load. Also, lateral deflections, cracking loads, and ultimate loads of identical loads tested under one-way and two-way action are compared.

Stiffened composite cylindrical panels�Optimum lay-up for buckling by ranking

Buckling of discretely stiffened composite cylindrical panels made of repeated sublaminate construction is studied using a finite element method. In repeated sublaminate construction, a full laminate is obtained by repeating a basic sublaminate, which has a smaller number of plies. This paper deals with the determination of the optimum lay-up for buckling by ranking of such stiffened (longitudinal and hoop) composite cylindrical panels. For this purpose we use the particularized form of a four-noded, 48 degrees of freedom doubly curved quadrilateral thin shell finite element together with a fully compatible two-noded, 16 degrees of freedom composite stiffener element. The computer program developed has been used, after extensive checking for correctness, to obtain an optimum orientation scheme of the plies in the sublaminate so as to achieve maximum buckling load for a specified thickness of typical stiffened composite cylindrical panels.

PRUNE and PROBE-two modular web services for protein-protein docking

The protein-protein docking programs typically perform four major tasks: (i) generation of docking poses, (ii) selecting a subset of poses, (iii) their structural refinement and (iv) scoring, ranking for the final assessment of the true quaternary structure. Although the tasks can be integrated or performed in a serial order, they are by nature modular, allowing an opportunity to substitute one algorithm with another. We have implemented two modular web services, (i) PRUNE: to select a subset of docking poses generated during sampling search (http://pallab.serc.iisc.ernet.in/prune) and (ii) PROBE: to refine, score and rank them (http://pallab.serc.iisc.ernet.in/probe). The former uses a new interface area based edge-scoring function to eliminate > 95% of the poses generated during docking search. In contrast to other multi-parameter-based screening functions, this single parameter based elimination reduces the computational time significantly, in addition to increasing the chances of selecting native-like models in the top rank list. The PROBE server performs ranking of pruned poses, after structure refinement and scoring using a regression model for geometric compatibility, and normalized interaction energy. While web-service similar to PROBE is infrequent, no web-service akin to PRUNE has been described before. Both the servers are publicly accessible and free for use.

DEPTH: a web server to compute depth and predict small-molecule binding cavities in proteins

Depth measures the extent of atom/residue burial within a protein. It correlates with properties such as protein stability, hydrogen exchange rate, protein-protein interaction hot spots, post-translational modification sites and sequence variability. Our server, DEPTH, accurately computes depth and solvent-accessible surface area (SASA) values. We show that depth can be used to predict small molecule ligand binding cavities in proteins. Often, some of the residues lining a ligand binding cavity are both deep and solvent exposed. Using the depth-SASA pair values for a residue, its likelihood to form part of a small molecule binding cavity is estimated. The parameters of the method were calibrated over a training set of 900 high-resolution X-ray crystal structures of single-domain proteins bound to small molecules (molecular weight < 1.5 KDa). The prediction accuracy of DEPTH is comparable to that of other geometry-based prediction methods including LIGSITE, SURFNET and Pocket-Finder (all with Matthew's correlation coefficient of similar to 0.4) over a testing set of 225 single and multi-chain protein structures. Users have the option of tuning several parameters to detect cavities of different sizes, for example, geometrically flat binding sites. The input to the server is a protein 3D structure in PDB format. The users have the option of tuning the values of four parameters associated with the computation of residue depth and the prediction of binding cavities. The computed depths, SASA and binding cavity predictions are displayed in 2D plots and mapped onto 3D representations of the protein structure using Jmol. Links are provided to download the outputs. Our server is useful for all structural analysis based on residue depth and SASA, such as guiding site-directed mutagenesis experiments and small molecule docking exercises, in the context of protein functional annotation and drug discovery.