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  1. null (Ed.)
  2. null (Ed.)
  3. Xu, Jinbo (Ed.)
    Abstract Summary Spectroscopic single-molecule localization microscopy (sSMLM) simultaneously captures the spatial locations and full spectra of stochastically emitting fluorescent single molecules. It provides an optical platform to develop new multimolecular and functional imaging capabilities. While several open-source software suites provide subdiffraction localization of fluorescent molecules, software suites for spectroscopic analysis of sSMLM data remain unavailable. RainbowSTORM is an open-source ImageJ/FIJI plug-in for end-to-end spectroscopic analysis and visualization for sSMLM images. RainbowSTORM allows users to calibrate, preview and quantitatively analyze emission spectra acquired using different reported sSMLM system designs and fluorescent labels. Availability and implementation RainbowSTORM is a java plug-in for ImageJ ( ( freely available through: RainbowSTORM has been tested with Windows and Mac operating systems and ImageJ/FIJI version 1.52. Supplementary information Supplementary data are available at Bioinformatics online. 
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  4. Abstract Motivation The success of genome sequencing techniques has resulted in rapid explosion of protein sequences. Collections of multiple homologous sequences can provide critical information to the modeling of structure and function of unknown proteins. There are however no standard and efficient pipeline available for sensitive multiple sequence alignment (MSA) collection. This is particularly challenging when large whole-genome and metagenome databases are involved. Results We developed DeepMSA, a new open-source method for sensitive MSA construction, which has homologous sequences and alignments created from multi-sources of whole-genome and metagenome databases through complementary hidden Markov model algorithms. The practical usefulness of the pipeline was examined in three large-scale benchmark experiments based on 614 non-redundant proteins. First, DeepMSA was utilized to generate MSAs for residue-level contact prediction by six coevolution and deep learning-based programs, which resulted in an accuracy increase in long-range contacts by up to 24.4% compared to the default programs. Next, multiple threading programs are performed for homologous structure identification, where the average TM-score of the template alignments has over 7.5% increases with the use of the new DeepMSA profiles. Finally, DeepMSA was used for secondary structure prediction and resulted in statistically significant improvements in the Q3 accuracy. It is noted that all these improvements were achieved without re-training the parameters and neural-network models, demonstrating the robustness and general usefulness of the DeepMSA in protein structural bioinformatics applications, especially for targets without homologous templates in the PDB library. Availability and implementation Supplementary information Supplementary data are available at Bioinformatics online. 
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  5. Since the discovery of the B 40 borospherene, research interests have been directed to the structural evolution of even larger boron clusters. An interesting question concerns if the borospherene cages persist in larger boron clusters like the fullerenes. Here we report a photoelectron spectroscopy (PES) and computational study on the structures and bonding of B 41 − and B 42 − , the largest boron clusters characterized experimentally thus far. The PE spectra of both clusters display broad and complicated features, suggesting the existence of multiple low-lying isomers. Global minimum searches for B 41 − reveal three low-lying isomers ( I–III ), which are all related to the planar B 40 − structure. Isomer II ( C s , 1 A′) possessing a double hexagonal vacancy is found to agree well with the experiment, while isomers I ( C s , 3 A′′) and III ( C s , 1 A′) both with a single hexagonal vacancy are also present as minor isomers in the experiment. The potential landscape of B 42 − is found to be much more complicated with numerous low-lying isomers ( VII–XII ). The quasi-planar structure VIII ( C 1 , 2 A) containing a double hexagonal vacancy is found to make major contributions to the observed PE spectrum of B 42 − , while the other low-lying isomers may also be present to give rise to a complicated spectral pattern. Chemical bonding analyses show isomer II of B 41 − ( C s , 1 A′) and isomer VIII of B 42 − ( C 1 , 2 A) are π aromatic, analogous to that in the polycyclic aromatic hydrocarbon C 27 H 13 + ( C 2v , 1 A 1 ). Borospherene cage isomers are also found for both B 41 − and B 42 − in the global minimum searches, but they are much higher energy isomers. 
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