ConSole: using modularity of contact maps to locate solenoid domains in protein structures.

BackgroundPeriodic proteins, characterized by the presence of multiple repeats of short motifs, form an interesting and seldom-studied group. Due to often extreme divergence in sequence, detection and analysis of such motifs is performed more reliably on the structural level. Yet, few algorithms have been developed for the detection and analysis of structures of periodic proteins.ResultsConSole recognizes modularity in protein contact maps, allowing for precise identification of repeats in solenoid protein structures, an important subgroup of periodic proteins. Tests on benchmarks show that ConSole has higher recognition accuracy as compared to Raphael, the only other publicly available solenoid structure detection tool. As a next step of ConSole analysis, we show how detection of solenoid repeats in structures can be used to improve sequence recognition of these motifs and to detect subtle irregularities of repeat lengths in three solenoid protein families.ConclusionsThe ConSole algorithm provides a fast and accurate tool to recognize solenoid protein structures as a whole and to identify individual solenoid repeat units from a structure. ConSole is available as a web-based, interactive server and is available for download at http://console.sanfordburnham.org

Cancer3D: understanding cancer mutations through protein structures.

The new era of cancer genomics is providing us with extensive knowledge of mutations and other alterations in cancer. The Cancer3D database at http://www.cancer3d.org gives an open and user-friendly way to analyze cancer missense mutations in the context of structures of proteins in which they are found. The database also helps users analyze the distribution patterns of the mutations as well as their relationship to changes in drug activity through two algorithms: e-Driver and e-Drug. These algorithms use knowledge of modular structure of genes and proteins to separately study each region. This approach allows users to find novel candidate driver regions or drug biomarkers that cannot be found when similar analyses are done on the whole-gene level. The Cancer3D database provides access to the results of such analyses based on data from The Cancer Genome Atlas (TCGA) and the Cancer Cell Line Encyclopedia (CCLE). In addition, it displays mutations from over 14,700 proteins mapped to more than 24,300 structures from PDB. This helps users visualize the distribution of mutations and identify novel three-dimensional patterns in their distribution

PDBFlex: exploring flexibility in protein structures.

The PDBFlex database, available freely and with no login requirements at http://pdbflex.org, provides information on flexibility of protein structures as revealed by the analysis of variations between depositions of different structural models of the same protein in the Protein Data Bank (PDB). PDBFlex collects information on all instances of such depositions, identifying them by a 95% sequence identity threshold, performs analysis of their structural differences and clusters them according to their structural similarities for easy analysis. The PDBFlex contains tools and viewers enabling in-depth examination of structural variability including: 2D-scaling visualization of RMSD distances between structures of the same protein, graphs of average local RMSD in the aligned structures of protein chains, graphical presentation of differences in secondary structure and observed structural disorder (unresolved residues), difference distance maps between all sets of coordinates and 3D views of individual structures and simulated transitions between different conformations, the latter displayed using JSMol visualization software

Effects of Processing on Microstructure and Mechanical Properties of Ti-6Al-4V Fabricated using Electron Beam Melting (EBM): Orientation and Location

Electron beam melted (EBM) titanium alloy (Ti-6Al-4V) samples were built and characterized (qualitative prior-β grain size, quantitative α lath thickness, monotonic tensile, Vickers microhardness) to determine the effect of location and orientation on microstructure and properties. Samples of vertical orientation, compared to horizontal, were found to have 30% lower elongation. Orientation within the x-y plane as well as location were found to have less than 3 % effect on mechanical properties, and it is possible a second order effect of thermal mass contributed to these results.Mechanical Engineerin

3D image analysis of the shapes and dimensions of several tropical fruits

ArticleT hree dimension virtual models of Avocado ( Persea americana ) , Salak ( Salacca zalacca ) , Dragon fruit ( Hylocereus undatus ) , Mango ( Mangifera indica ) , Coconut ( Cocos nucifera ) using 3D scanner Intel RealSense were determined. C alculated models based on arithmetic and geometric diameter were also determined. From statistically analysis implies that virtual models on significance level 0 .05 are significantly different with calculated values based on arithmetic or geometric diameter

Utilization of image analysis for description of drying characteristics of selected tropical fruits

ArticleThis study is focused on the utilization of image analysis for description of dimensions, and colours changes of fruits during drying process. Selected tropical fruits such are banana (Musa acuminata), mango (Magnifera indica) and pineapple (Ananas comosus) originally from North Sumatera in Indonesia were used in this experiment. Sliced pieces of the fruits were dried in experimental oven under temperature 90 °C for period of time 180 min and image of fruits samples were recorded by digital camera with HD resolution continuously throughout drying process. With aid of image analysis using Image J software and regarding to drying characteristics the colours and dimensions of the samples were analysed

Theoretical analysis of force, pressure and energy distributions of bulk oil palm kernels along the screwline of a mechanical screw press FL 200

ArticleThe present study is a follow-up of the previously published study on the mathematical description of loading curves and deformation energy of bulk oil palm kernels under compression loading, aimed at determining theoretically the amounts of force, pressure and energy along the screw lamella positions of the screw press FL 200 by applying the tangent curve mathematical model and the screwline geometry parameters (screw shaft diameter, screw inner and outer diameters, screw pitch diameter and the screw thickness). The fitting curve value of the tangent mathematical model was further examined at = 2 and = 3 by identifying the force, deformation, stress and compression coefficients at varying vessel diameters and initial pressing heights of the bulk oil palm kernels. Based on the results of the stepwise regression analysis, the amounts of the theoretical deformation energy in linear pressing as well as the theoretical force , pressure and energy of the screw press FL 200 were statistically significant (P-value significance F) in relation to the predictors ( , , and ). The coefficient of determination (R2 ) values between 61 and 86 % were observed for the determined regression models indicating that the responses , , and can accurately be predicted by the corresponding predictors. The normal probability plots of the responses approximately showed a normal distribution

Mathematical description of loading curves and deformation energy of bulk oil palm kernels

ArticleThe study aimed at describing the experimental and theoretical relationships between t he force and deformation curves as well as the deformation energy of bulk oil palm kernels under compression loading. V essel diameters of 60, 80 and 100 mm with initial pressing heights of the bulk kernels measured at 40, 60 and 80 mm were examined by appl ying a maximum compressive force of 200 kN and a speed of 5 mm min - 1 . For the theoretical description of the force and deformation curves, the tangent curve mathematical model was applied using the MathCAD 14 software where the force coefficient of mechani cal behaviour, A (kN), the deformation coefficient of mechanical behaviour, B (mm - 1 ) and the fitting curve function exponent, n ( - ) were determined respectively. The determined coefficients in addition to the maximum deformation values obtained from the co mpression test were used for the estimation of the theoretical or analytical deformation energy. The determined regression models expressing the deformation, numerical energy and theoretical energy as well as the tangent model coefficients A and B dependen t on the vessel diameter and pressing height were statistically significant ( P < 0.05) or ( F - ratio > F - critical) . Improving the mechanical pressing of oil extraction for both domestic and industrial applications still remain a concer n of researchers and en gineers