HyPaLib: a database of RNAs and RNA structural elements defined by hybrid patterns

The database, called HyPaLib (for Hybrid Pattern Library), contains annotated structural elements characteristic for certain classes of structural and/or functional RNAs. These elements are described in a language specifically designed for this purpose. The language allows convenient specification of hybrid patterns, i.e. motifs consisting of sequence features and structural elements together with sequence similarity and thermodynamic constraints. We are currently developing software tools that allow a user to search sequence databases for any pattern in HyPaLib, thus providing functionality which is similar to PROSITE, but dedicated to the more complex patterns in RNA sequences. HyPaLib is available at http://bibiserv.techfak.uni-bielefeld.de/HyPa/.

Face authentication test on the BANCA database

This work details the results of a face authentication test (FAT2004) (http://www.ee.surrey.ac.uk/banca/icpr2004) held in conjunction with the 17th International Conference on Pattern Recognition. The contest was held on the publicly available BANCA database (http://www.ee.surrey.ac.uk/banca) according to a defined protocol (E. Bailly-Bailliere et al., June 2003). The competition also had a sequestered part in which institutions had to submit their algorithms for independent testing. 13 different verification algorithms from 10 institutions submitted results. Also, a standard set of face recognition software packages from the Internet (http://www.cs.colostate.edu/evalfacerec) were used to provide a baseline performance measure.

Engineering the mechanical properties of graphene nanotube hybrid structures through structural modulation

The excellent multi-functional properties of carbon nanotube (CNT) and graphene have enabled them as appealing building blocks to construct 3D carbon-based nanomaterials or nanostructures. The recently reported graphene nanotube hybrid structure (GNHS) is one of the representatives of such nanostructures. This work investigated the relationships between the mechanical properties of the GNHS and its structure basing on large-scale molecular dynamics simulations. It is found that increasing the length of the constituent CNTs, the GNHS will have a higher Young’s modulus and yield strength. Whereas, no strong correlation is found between the number of graphene layers and Young’s modulus and yield strength, though more graphene layers intends to lead to a higher yield strain. In the meanwhile, the presences of multi-wall CNTs are found to greatly strengthen the hybrid structure. Generally, the hybrid structures exhibit a brittle behavior and the failure initiates from the connecting regions between CNT and graphene. More interestingly, affluent formations of monoatomic chains and rings are found at the fracture region. This study provides an in-depth understanding of the mechanical performance of the GNHSs while varying their structures, which will shed lights on the design and also the applications of the carbon-based nanostructures.

MLDB: macromolecule ligand database

MLDB (macromolecule ligand database) is a knowledge base containing ligands co-crystallized with the three-dimensional structures available in the Protein Data Bank. The proposed knowledge base serves as an open resource for the analysis and visualization of all ligands and their interactions with macromolecular structures. MLDB can be used to search ligands, and their interactions can be visualized both in text and graphical formats. MLDB will be updated at regular intervals (weekly) with automated Perl scripts. The knowledge base is intended to serve the scientific community working in the areas of molecular and structural biology. It is available free to users around the clock and can be accessed at http://dicsoft2.physics.iisc.ernet.in/mldb/.

CancerLectinDB: a database of lectins relevant to cancer

The role of lectins in mediating cancer metastasis, apoptosis as well as various other signaling events has been well established in the past few years. Data on various aspects of the role of lectins in cancer is being accumulated at a rapid pace. The data on lectins available in the literature is so diverse, that it becomes difficult and time-consuming, if not impossible to comprehend the advances in various areas and obtain the maximum benefit. Not only do the lectins vary significantly in their individual functional roles, but they are also diverse in their sequences, structures, binding site architectures, quaternary structures, carbohydrate affinities and specificities as well as their potential applications. An organization of these seemingly independent data into a common framework is essential in order to achieve effective use of all the data towards understanding the roles of different lectins in different aspects of cancer and any resulting applications. An integrated knowledge base (CancerLectinDB) together with appropriate analytical tools has therefore been developed for lectins relevant for any aspect of cancer, by collating and integrating diverse data. This database is unique in terms of providing sequence, structural, and functional annotations for lectins from all known sources in cancer and is expected to be a useful addition to the number of glycan related resources now available to the community. The database has been implemented using MySQL on a Linux platform and web-enabled using Perl-CGI and Java tools. Data for individual lectins pertain to taxonomic, biochemical, domain architecture, molecular sequence and structural details as well as carbohydrate specificities. Extensive links have also been provided for relevant bioinformatics resources and analytical tools. Availability of diverse data integrated into a common framework is expected to be of high value for various studies on lectin cancer biology.

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/.

Studies on molecular evolution and structural features of double-headed inhibitors of ?-amylase and trypsin in plants

Plant seeds usually have high concentrations of proteinase and amylase inhibitors. These inhibitors exhibit a wide range of specificity, stability and oligomeric structure. In this communication, we report analysis of sequences that show statistically significant similarity to the double-headed alpha-amylase/trypsin inhibitor of ragi (Eleusine coracana). Our aim is to understand their evolutionary and structural features. The 14 sequences of this family that are available in the SWISSPROT database form three evolutionarily distinct branches. The branches relate to enzyme specificities and also probably to the oligomeric state of the proteins and not to the botanical class of the plant from which the enzymes are derived. This suggests that the enzyme specificities of the inhibitors evolved before the divergence of commercially cultivated cereals. The inhibitor sequences have three regions that display periodicity in hydrophobicity. It is likely that this feature reflects extended secondary structure in these segments. One of the most variable regions of the polypeptide corresponds to a loop, which is most probably exposed in the native structure of the inhibitors and is responsible for the inhibitory property.

Structural and dielectric properties of Bi2NbxV1-xO5.5 ceramics

Bi2NbxV1-xO5.5 ceramics with x ranging from 0.01 to 0.5 have been prepared. The crystal system transforms from an orthorhombic to tetragonal at x greater than or equal to 0.1 and it persists until x = 0.5. Scanning electron microscopic (SEM) investigations carried out on thermally etched Bi2NbxV1-xO5.5 ceramics confirm that the grain size decreases markedly (18 mu m to 4 mu m) with increasing x. The shift in the Curie temperature (725 K) toward lower temperatures, with increasing x, is established by Differential Scanning Calorimetry (DSC). The dielectric constants as well as the loss tangent (tan delta) decrease with increasing x at room temperature.

Structural and dielectric properties of Bi2NbxVi−xO5.5 ceramics

Bi2Nbx V1−xO5.5 ceramics with x ranging from 0.01 to 0.5 have been prepared. The crystal system transforms from an orthorhombic to tetragonal at x 3= 0.1 and it persists until x = 0.5. Scanning electron microscopic (SEM) investigations carried out on thermally etched Bi2NbxV1−xO5.5 ceramics confirm that the grain size decreases markedly (18 μm to 4 μm) with increasing x. The shift in the Curie temperature (725 K) toward lower temperatures, with increasing x, is established by Differential Scanning Calorimetry (DSC). The dielectric constants as well as the loss tangent (tan δ) decrease with increasing x at room temperature.

Structural Relaxation and Crystallization in a Pd40Cu30Ni10P20 Bulk Metallic Glass

The stability of a Pd40Cu30Ni10P20 bulk metallic glass (BMG) against structural relaxation is investigated by isothermal and isochronal annealing heat treatments below and above its glass transition temperature, Tg, for varying periods. Differential scanning calorimetry (DSC) of the annealed samples shows an excess endotherm at Tg, irrespective of the annealing temperature. This recovery peak evolves exponentially with annealing time and is due to the destruction of anneal-induced compositional short range ordering. The alloy exhibits a high resistance to crystallization on annealing below Tg and complex Pd- and Ni-phosphides evolve on annealing above Tg.

Tailoring of Structural Morphology of Silver Nanowires in Electrochemical Growth

Noble metal such as Ag normally exists in an fcc crystal structure. However as the size of the material is decreased to nanometer lengthscales, a structural transformation from that of its bulk state can be expected with new atomic arrangements due to competition between internal packing and minimization of surface energy. In many previous studies, it has been shown that silver nanowires (AGNWs) grown inside anodic alumina (AAO) templates by ac or dc electrochemical deposition from silver salts or complexes, adopt fcc structure and below some critical diameter ∼ 20 nm they may acquire hcp structure at low temperature. This is, however, critically dependant on the nature of confinement, as AgNWs grown inside nanotube confinement with subnanometer diameter have been reported to have fcc structure. Hence the question of the crystal structure of metal nanowires under combined influence of confinement, temperature and deposition condition remains open. In this abstract we show that the alternative crystal structures of AGNWs at room temperature can be achieved with electrochemical growth processes under specific conditions determined by the deposition parameters and nature of confinement. We fabricated AgNWs of 4H hexagonal structure with diameters 30 – 80 nm inside polycarbonate (PC) templates with a modified dc electrodeposition technique, where the nanowires were grown at deposition potentials as low as 10 mV in 2 M silver nitrate solution[1]. We call this low-potential electrodeposition (LPED) since the electrodeposition process occurs at potential much less than the standard Nernst potential (770 mV) of silver. Two types of electrodes were used – stainless steel and sputtered thin Pt film, neither of which had any influence on the crystal structure of the nanowires. EDS elemental analysis showed the nanowires to consist only of silver. Although the precise atomic dynamics during the LPED process is unclear at present, we investigated this with HRTEM (high-resolution transmission electron microscopy) characterization of nanowires grown over various deposition times, as well as electrical conductivity measurements. These experiments indicate that nanowire growth does not occur through a three-dimensional diffusion controlled process, as proposed for conventional over-potential deposition, but follow a novel instantaneous linear growth mechanism. Further experiments showed that, (a) conventional electrochemical growth at a small over-potential in a 2 mM AgNO3 solution yields nanowires with expected fcc structure inside the same PC templates, and (2) no nanowire was observed under the LPED conditions inside hard AAO templates, indicating that LPED-growth process, and hcp structure of the corresponding nanowires depend on deposition parameters, as well as nature of confinement.

Structural, optical and nanomechanical properties of (1 1 1) oriented nanocrystalline ZnTe thin films

Structural, optical and nanomechanical properties of nanocrystalline Zinc Telluride (ZnTe) films of thickness upto 10 microns deposited at room temperature on borosilicate glass substrates are reported. X-ray diffraction patterns reveal that the films were preferentially oriented along the (1 1 1) direction. The maximum refractive index of the films was 2.74 at a wavelength of 2000 nm. The optical band gap showed strong thickness dependence. The average film hardness and Young's modulus obtained from load-displacement curves and analyzed by Oliver-Pharr method were 4 and 70 GPa respectively. Hardness of (1 1 1) oriented ZnTe thin films exhibited almost 5 times higher value than bulk. The studies show clearly that the hardness increases with decreasing indentation size, for indents between 30 and 300 nm in depth indicating the existence of indentation size effect. The coefficient of friction for these films as obtained from the nanoscratch test was ~0.4.

Structural, optical and nanomechanical properties of (1 1 1) oriented nanocrystalline ZnTe thin films

Structural, optical and nanomechanical properties of nanocrystalline Zinc Telluride (ZnTe) films of thickness upto 10 microns deposited at room temperature on borosilicate glass substrates are reported. X-ray diffraction patterns reveal that the films were preferentially oriented along the (1 1 1) direction. The maximum refractive index of the films was 2.74 at a wavelength of 2000 nm. The optical band gap showed strong thickness dependence. The average film hardness and Young's modulus obtained from load-displacement curves and analyzed by Oliver-Pharr method were 4 and 70 GPa respectively. Hardness of (1 1 1) oriented ZnTe thin films exhibited almost 5 times higher value than bulk. The studies show clearly that the hardness increases with decreasing indentation size, for indents between 30 and 300 nm in depth indicating the existence of indentation size effect. The coefficient of friction for these films as obtained from the nanoscratch test was ~0.4.

Structural landscape of benzoic acid: using experimental crystal structures of fluorobenzoic acids as a probe

Experimental crystal structures of mono and polyfluorinated benzoic acids correspond to high energy computed crystal structures of benzoic acid itself, thereby permitting access to its structural landscape.

Combinatorial Exploration of the Structural Landscape of Acid-Pyridine Cocrystals

The structural landscape of acid-pyridine cocrystals is explored by adopting a combinatorial matrix method with 4-substituted benzoic acids and 4-substituted pyridines. The choice of the system restricts the primary synthon to the robust acid-pyridine entity. This methodology accordingly provides hints toward the formation of secondary synthons. The pK(a) rule is validated in the landscape by taking all components of the matrix together and exploring it as a whole. Along with the global features, the exploration of landscapes reveals some local features. Apart from the identification of secondary synthons, it also sheds light on the propensity of hydration in cocrystals, synthon competition, and certain topological similarities. The method described here combines two approaches, namely, database analysis and high throughput crystallography, to extract more information with minimal extra experimental effort.