Search results for "Database"
showing 10 items of 2136 documents
String kernels and high-quality data set for improved prediction of kinked helices in α-helical membrane proteins.
2011
The reasons for distortions from optimal α-helical geometry are widely unknown, but their influences on structural changes of proteins are significant. Hence, their prediction is a crucial problem in structural bioinformatics. For the particular case of kink prediction, we generated a data set of 132 membrane proteins containing 1014 manually labeled helices and examined the environment of kinks. Our sequence analysis confirms the great relevance of proline and reveals disproportionately high occurrences of glycine and serine at kink positions. The structural analysis shows significantly different solvent accessible surface area mean values for kinked and nonkinked helices. More important, …
Exploiting a list of protein sequences
2007
Abstract: We describe a software program to help exploit a database of aligned protein sequences. In addition to the classical lists of sequences, a graphical representation is used to get a better overview of the information. As natural parameters, the type of amino acid and sequence position are used. Various plots or 3D representations are then updated. Examples are shown based on globin sequences from various species and on the abnormal human hemoglobins. The software should be of interest to protein engineers who need to know what variants are already known.
Efficient virtual screening using multiple protein conformations described as negative images of the ligand-binding site.
2010
The protein structure-based virtual screening is typically accomplished using a molecular docking procedure. However, docking is a fairly slow process that is limited by the available scoring functions that cannot reliably distinguish between active and inactive ligands. In contrast, the ligand-based screening methods that are based on shape similarity identify the active ligands with high accuracy. Here, we show that the usage of negative images of the ligand-binding site, together with shape comparison tools, which are typically used in ligand-based virtual screening, improve the discrimination of active molecules from inactives. In contrast to ligand-based shape comparison, the negative …
Protein knot server: detection of knots in protein structures
2007
KNOTS (http://knots.mit.edu) is a web server that detects knots in protein structures. Several protein structures have been reported to contain intricate knots. The physiological role of knots and their effect on folding and evolution is an area of active research. The user submits a PDB id or uploads a 3D protein structure in PDB or mmCIF format. The current implementation of the server uses the Alexander polynomial to detect knots. The results of the analysis that are presented to the user are the location of the knot in the structure, the type of the knot and an interactive visualization of the knot. The results can also be downloaded and viewed offline. The server also maintains a regul…
NightShift: NMR shift inference by general hybrid model training--a framework for NMR chemical shift prediction.
2012
Background NMR chemical shift prediction plays an important role in various applications in computational biology. Among others, structure determination, structure optimization, and the scoring of docking results can profit from efficient and accurate chemical shift estimation from a three-dimensional model. A variety of NMR chemical shift prediction approaches have been presented in the past, but nearly all of these rely on laborious manual data set preparation and the training itself is not automatized, making retraining the model, e.g., if new data is made available, or testing new models a time-consuming manual chore. Results In this work, we present the framework NightShift (NMR Shift …
Variation of the BrO/SO2 molar ratio in the plume of Tungurahua volcano between 2007 and 2017 and its relationship to volcanic activity
2019
International audience; Recent long-term observations of the bromine monoxide (BrO) to sulphur dioxide (SO2) molar ratio in volcanic plumes have suggested a link between changes in the BrO/SO2 ratio and the volcanic activity. Nevertheless, understanding of the mechanisms determining this link is still limited due to the lack of studies on volcanic bromine release from the melt into the atmosphere. We present the results of 10 years (2007–2017) of observations of the BrO/SO2 molar ratio in the volcanic plume of Tungurahua volcano, Ecuador. Following the nearly continuous eruptive activity from 1999 to 2008, Tungurahua showed alternating phases of eruptive activity separated by periods of qui…
Context-Aware Visual Exploration of Molecular Databases
2006
Facilitating the visual exploration of scientific data has\ud received increasing attention in the past decade or so. Especially\ud in life science related application areas the amount\ud of available data has grown at a breath taking pace. In this\ud paper we describe an approach that allows for visual inspection\ud of large collections of molecular compounds. In\ud contrast to classical visualizations of such spaces we incorporate\ud a specific focus of analysis, for example the outcome\ud of a biological experiment such as high throughout\ud screening results. The presented method uses this experimental\ud data to select molecular fragments of the underlying\ud molecules that have intere…
Synthesis and characterization of novel bile-acid – heteroaryl conjugates with N-(2-aminoethyl)amido linker
2008
Abstract Four novel bile acid conjugates N-[2-([2,2′]-bithiophen-5-ylmethyl)aminoethyl]-3α-hydroxy-5β-cholan-24-amide (1), N-[2-([2,2′]-bithiophen-5-ylmethyl)aminoethyl]-3α,7α,12α-trihydroxy-5β-cholan-24-amide (2), N-[2-(1H-pyrrol-2-ylmethyl)aminoethyl]-3α-hydroxy-5β-cholan-24-amide (3), N-[2-(pyridin-2-ylmethyl)aminoethyl]-3α-hydroxy-5β-cholan-24-amide (4) have been synthesized in moderate to good yields, and their structures have been characterized by 1H, 13C, 13C DEPT-135, PFG 1H,13C HMQC, and PFG 1H,13C HMBC NMR spectra. Their molecular weights and elemental compositions have been determined by ESI-TOF mass spectrometry and elemental analyses. Crystal structure of 1 characterized with o…
Automatic detection and analysis of cell motility in phase-contrast time-lapse images using a combination of maximally stable extremal regions and Ka…
2013
Phase-contrast illumination is simple and most commonly used microscopic method to observe nonstained living cells. Automatic cell segmentation and motion analysis provide tools to analyze single cell motility in large cell populations. However, the challenge is to find a sophisticated method that is sufficiently accurate to generate reliable results, robust to function under the wide range of illumination conditions encountered in phase-contrast microscopy, and also computationally light for efficient analysis of large number of cells and image frames. To develop better automatic tools for analysis of low magnification phase-contrast images in time-lapse cell migration movies, we investiga…
Near Real-Time Data Warehousing with Multi-stage Trickle and Flip
2011
A data warehouse typically is a collection of historical data designed for decision support, so it is updated from the sources periodically, mostly on a daily basis. Today’s business however asks for fresher data. Real-time warehousing is one of the trends to accomplish this, but there are a number of challenges to move towards true real-time. This paper proposes ‘Multi-stage Trickle & flip’ methodology for data warehouse refreshment. It is based on the ‘Trickle & flip’ principle and extended in order to further insulate loading and querying activities, thus enabling both of them to be more efficient.