The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases

The SIB Swiss Institute of Bioinformatics (www.isb-sib.ch) provides world-class bioinformatics databases, software tools, services and training to the international life science community in academia and industry. These solutions allow life scientists to turn the exponentially growing amount of data into knowledge. Here, we provide an overview of SIB's resources and competence areas, with a strong focus on curated databases and SIB's most popular and widely used resources. In particular, SIB's Bioinformatics resource portal ExPASy features over 150 resources, including UniProtKB/Swiss-Prot, ENZYME, PROSITE, neXtProt, STRING, UniCarbKB, SugarBindDB, SwissRegulon, EPD, arrayMap, Bgee, SWISS-MODEL Repository, OMA, OrthoDB and other databases, which are briefly described in this article

Global analysis of the CD2HOH molecule rotation-torsion spectrum

International audienc

The Water Molecule: Line Position and Line Intensity Analyses up to the Second Triad

With a view towards building a highly accurate database for the water molecule in the 1000 to 2000 cm -1 region, line position and line intensity analyses of a large body of high-resolution data were carried out. For both analyses, the bending-rotation theoretical approach 1 was used. The body of data fitted in the line position analysis consists of experimental energies as well as microwave, FIR, and IR transitions. In the line strength analysis, experimental line intensities were fitted. For both analyses, the data involve the first eight vibrational states of water, that is, all the vibrational states up to the second triad. In the first part of the paper, the results of the line position analysis will be reported and the inclusion in the data set of the recent microwave measurements of Matsushima et al. 2 will be discussed. The second part of the paper we will devoted to the line strength analysis. The results obtained fitting the new measurements of Toth 3 , concern- ing transitions involving one the states of the second triad, will be reported. Although the results of both the line position and the line intensity analyses are satisfactory, they indicate that there are inconsistencies within and between the various sets of of data. This is certainly the case of the line intensity data for transitions belonging to the ? 2 band, which is the band for which there is the largest amount of data. For this band the measurements reported by Toth 4 are available as well as the recent ones carried out at DLR. Depending on the set of data being considered, the observed minus calculated residuals, in % of the observed strength, do not display the same behavior when the strength increases from 10 -25 to 10 -19 cm -1/molecule ú cm -2 . This behavior will be given for the line strengths reported by Toth 4 and for those measured in the present work. Issues addressing the data quality and reasons for the di’erences of the data sets will be discussed

Line Position and Line Intensity Modelings of H218O up to the First Triad and J = 20

International audienceLine position and line intensity analyses are carried out for the H218O isotopic species of the water molecule. Both datasets involve the five lowest lying vibrational states. For the line position analysis, the dataset includes infrared and far infrared transitions recorded in this work using high-temperature Fourier transform emission spectroscopy. Also included are already published infrared, far infrared, microwave, terahertz, Doppler-free combination differences, and kHz accuracy lines. The fitting is carried out with the bending–rotation approach and allows us to reproduce 12 858 line positions involving levels with J ≤ 20 and Ka ≤ 18, with a unitless standard deviation of 1.9, varying 207 spectroscopic parameters. For the line intensity analysis, far infrared line intensities measured in this work using Fourier transform spectroscopy in addition to previously measured line intensities are fitted. 5612 line intensities are accounted for with a unitless standard deviation of 1.5. The results from both analyses are used to build a line list for atmospherical purposes, spanning the 2–5000 cm−1 spectral range and containing 7593 lines. This line list and calculated energies and line intensities are compared to those already published

Experimental and theoretical investigations of H2O-Ar

We have used continuous-wave cavity ring-down spectroscopy to record the spectrum of H2O-Ar in the 2OH excitation range of H2O. 24 sub-bands have been observed. Their rotational structure (Trot = 12 K) is analyzed and the lines are fitted separately for ortho and para species together with microwave and far infrared data from the literature, with a unitless standard deviation σ=0.98 and 1.31, respectively. Their vibrational analysis is supported by a theoretical input based on an intramolecular potential energy surface obtained through ab initio calculations and computation of the rotational energy of sub-states of the complex with the water monomer in excited vibrational states up to the first hexad. For the ground and (010) vibrational states, the theoretical results agree well with experimental energies and rotational constants in the literature. For the excited vibrational states of the first hexad, they guided the assignment of the observed sub-bands. The upper state vibrational predissociation lifetime is estimated to be 3 ns from observed spectral linewidths.status: publishe

Ab Initio Intermolecular Potential of Ar–C₂H₂ Refined Using High-Resolution Spectroscopic Data

The high-resolution infrared spectra of the ν₁ + ν₃ (2CH) band of the Ar–C₂H₂ complex has been recorded from 6544 to 6566 cm^–1. The previously reported <i>K</i>_<i>a</i> = 1 ← 0, 2 ← 1, and 0 ← 1 subbands were observed and the <i>K</i>_<i>a</i> = 1 ← 2, 2 ← 3, and 3 ← 2 subbands were assigned for the first time. The intermolecular potential energy surface of this complex has been calculated ab initio and optimized by fitting the new high-resolution data. Refined intermolecular potential energy surfaces have been obtained for the ground vibrational state and for the excited <i>v</i>₁ = <i>v</i>₃ = 1 stretching state. For the former state, the results of the analysis are satisfactory and the microwave transitions of the complex are reproduced with a root-mean-square deviation of 5 MHz. For the latter state, systematic discrepancies arise in the analysis

Ab Initio Intermolecular Potential of Ar–C₂H₂ Refined Using High-Resolution Spectroscopic Data

The high-resolution infrared spectra of the ν₁ + ν₃ (2CH) band of the Ar–C₂H₂ complex has been recorded from 6544 to 6566 cm^–1. The previously reported <i>K</i>_<i>a</i> = 1 ← 0, 2 ← 1, and 0 ← 1 subbands were observed and the <i>K</i>_<i>a</i> = 1 ← 2, 2 ← 3, and 3 ← 2 subbands were assigned for the first time. The intermolecular potential energy surface of this complex has been calculated ab initio and optimized by fitting the new high-resolution data. Refined intermolecular potential energy surfaces have been obtained for the ground vibrational state and for the excited <i>v</i>₁ = <i>v</i>₃ = 1 stretching state. For the former state, the results of the analysis are satisfactory and the microwave transitions of the complex are reproduced with a root-mean-square deviation of 5 MHz. For the latter state, systematic discrepancies arise in the analysis