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  1. Free, publicly-accessible full text available January 1, 2023
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  3. iCn3D was initially developed as a web-based 3D molecular viewer. It then evolved from visualization into a full-featured interactive structural analysis software. It became a collaborative research instrument through the sharing of permanent, shortened URLs that encapsulate not only annotated visual molecular scenes, but also all underlying data and analysis scripts in a FAIR manner. More recently, with the growth of structural databases, the need to analyze large structural datasets systematically led us to use Python scripts and convert the code to be used in Node. js scripts. We showed a few examples of Python scripts at https://github.com/ncbi/icn3d/tree/master/icn3dpython to export secondary structures or PNG images from iCn3D. Users just need to replace the URL in the Python scripts to export other annotations from iCn3D. Furthermore, any interactive iCn3D feature can be converted into a Node. js script to be run in batch mode, enabling an interactive analysis performed on one or a handful of protein complexes to be scaled up to analysis features of large ensembles of structures. Currently available Node. js analysis scripts examples are available at https://github.com/ncbi/icn3d/tree/master/icn3dnode . This development will enable ensemble analyses on growing structural databases such as AlphaFold or RoseTTAFold on one hand and Electronmore »Microscopy on the other. In this paper, we also review new features such as DelPhi electrostatic potential, 3D view of mutations, alignment of multiple chains, assembly of multiple structures by realignment, dynamic symmetry calculation, 2D cartoons at different levels, interactive contact maps, and use of iCn3D in Jupyter Notebook as described at https://pypi.org/project/icn3dpy .« less
    Free, publicly-accessible full text available February 17, 2023
  4. Short (15–30 residue) chains of amino acids at the amino termini of expressed proteins known as signal peptides (SPs) specify secretion in living cells. We trained an attention-based neural network, the Transformer model, on data from all available organisms in Swiss-Prot to generate SP sequences. Experimental testing demonstrates that the model-generated SPs are functional: when appended to enzymes expressed in an industrial Bacillus subtilis strain, the SPs lead to secreted activity that is competitive with industrially used SPs. Additionally, the model-generated SPs are diverse in sequence, sharing as little as 58% sequence identity to the closest known native signal peptide and 73% ± 9% on average.
  5. In this demonstration, we present SpeakQL, a speech-driven query system and interface for structured data. SpeakQL supports a tractable and practically useful subset of regular SQL, allowing users to query in any domain with unbounded vocabulary with the help of speech/touch based user-in-the-loop mechanisms for correction. When querying in such domains, automatic speech recognition introduces countless forms of errors in transcriptions, presenting us with a technical challenge. We characterize such errors and leverage our observations along with SQL's unambiguous context-free grammar to first correct the query structure. We then exploit phonetic representation of the queried database to identify the correct Literals, hence delivering the corrected transcribed query. In this demo, we show that SpeakQL helps users reduce time and effort in specifying SQL queries significantly. In addition, we show that SpeakQL, unlike Natural Language Interfaces and conversational assistants, allows users to query over any arbitrary database schema. We allow the audience to explore SpeakQL using an easy-to-use web-based interface to compose SQL queries.