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  1. Since the 14th Critical Assessment of Techniques for Protein Structure Prediction (CASP14), AlphaFold2 has become the standard method for protein tertiary structure prediction. One remaining challenge is to further improve its prediction. We developed a new version of the MULTICOM system to sample diverse multiple sequence alignments (MSAs) and structural templates to improve the input for AlphaFold2 to generate structural models. The models are then ranked by both the pairwise model similarity and AlphaFold2 self-reported model quality score. The top ranked models are refined by a novel structure alignment-based refinement method powered by Foldseek. Moreover, for a monomer target that is a subunit of a protein assembly (complex), MULTICOM integrates tertiary and quaternary structure predictions to account for tertiary structural changes induced by protein-protein interaction. The system participated in the tertiary structure prediction in 2022 CASP15 experiment. Our server predictor MULTICOM_refine ranked 3rd among 47 CASP15 server predictors and our human predictor MULTICOM ranked 7th among all 132 human and server predictors. The average GDT-TS score and TM-score of the first structural models that MULTICOM_refine predicted for 94 CASP15 domains are ~0.80 and ~0.92, 9.6% and 8.2% higher than ~0.73 and 0.85 of the standard AlphaFold2 predictor respectively.

     
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    Free, publicly-accessible full text available December 1, 2024
  2. Free, publicly-accessible full text available September 1, 2024
  3. Free, publicly-accessible full text available July 29, 2024
  4. Abstract Motivation

    Proteins interact to form complexes to carry out essential biological functions. Computational methods such as AlphaFold-multimer have been developed to predict the quaternary structures of protein complexes. An important yet largely unsolved challenge in protein complex structure prediction is to accurately estimate the quality of predicted protein complex structures without any knowledge of the corresponding native structures. Such estimations can then be used to select high-quality predicted complex structures to facilitate biomedical research such as protein function analysis and drug discovery.

    Results

    In this work, we introduce a new gated neighborhood-modulating graph transformer to predict the quality of 3D protein complex structures. It incorporates node and edge gates within a graph transformer framework to control information flow during graph message passing. We trained, evaluated and tested the method (called DProQA) on newly-curated protein complex datasets before the 15th Critical Assessment of Techniques for Protein Structure Prediction (CASP15) and then blindly tested it in the 2022 CASP15 experiment. The method was ranked 3rd among the single-model quality assessment methods in CASP15 in terms of the ranking loss of TM-score on 36 complex targets. The rigorous internal and external experiments demonstrate that DProQA is effective in ranking protein complex structures.

    Availability and implementation

    The source code, data, and pre-trained models are available at https://github.com/jianlin-cheng/DProQA.

     
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  5. Free, publicly-accessible full text available March 31, 2024
  6. Su, Zhongqing ; Limongelli, Maria Pina ; Glisic, Branko (Ed.)
    The battery-powered wireless sensor network (WSN) is a promising solution for structural health monitoring (SHM) applications because of its low cost and easy installation capability. However, the long-term WSN operation suffers from various concerns related to uneven battery degradation of wireless sensors, associated battery management, and replacement requirement, and ensuring desired quality of service (QoS) of the WSN in practice. The battery life is one of the biggest limiting factors for long-term WSN operation. Considering the costly maintenance trips for battery replacement, a lack of effective battery degradation management at the system level can lead to a failure in WSN operation. Moreover, the QoS needs to be ensured under various practical uncertainties. Optimal selection with a maximal number of nodes in WSN under uncertainties is a critical task to ensure the desired QoS. This study proposes a reinforcement learning (RL) based framework for active control of the battery degradation at the WSN system level with the aim of the battery group replacement while extending the service life and ensuring the QoS of WSN. A comprehensive simulation environment was developed in a real-life WSN setup, i.e. WSN for a cable-stayed bridge SHM, considering various practical uncertainties. The RL agent was trained under a developed RL environment to learn optimal nodes and duty cycles, meanwhile managing battery health at the network level. In this study, a mode shape-based quality index is proposed for the demonstration. The training and test results showed the prominence of the proposed framework in achieving effective battery health management of the WSN for SHM. 
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    Free, publicly-accessible full text available April 18, 2024
  7. Free, publicly-accessible full text available May 1, 2024
  8. Abstract

    Five out of six La Niña events since 1998 have lasted two to three years. Why so many long-lasting multiyear La Niña events have emerged recently and whether they will become more common remains unknown. Here we show that ten multiyear La Niña events over the past century had an accelerated trend, with eight of these occurring after 1970. The two types of multiyear La Niña events over this time period followed either a super El Niño or a central Pacific El Niño. We find that multiyear La Niña events differ from single-year La Niñas by a prominent onset rate, which is rooted in the western Pacific warming-enhanced zonal advective feedback for the central Pacific multiyear La Niña events type and thermocline feedback for the super El Niño multiyear La Niña events type. The results from large ensemble climate simulations support the observed multiyear La Niña events–western Pacific warming link. More multiyear La Niña events will exacerbate adverse socioeconomic impacts if the western Pacific continues to warm relative to the central Pacific.

     
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