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BioProtIS: Streamlining protein-ligand interaction pipeline for analysis in genomic and transcriptomic exploration

JOURNAL OF MOLECULAR GRAPHICS & MODELLING 2024年 128卷 108721页

作者： Virgens, Graziela Soria Oliveira, Julia Cardoso, Maria Izadora Oliveira Teodoro, Joao Alfredo Amaral, Danilo T. Univ Fed ABC UFABC Ctr Ciencias Nat & Humanas Santo Andre SP Brazil Ave Estados 5001 Bloco A504-3 Room BR-09210580 Santo Andre Brazil

The identification of protein-ligand interactions plays a pivotal role in elucidating biological processes and discovering potential bioproducts. Harnessing the capabilities of computational methods in drug discovery, we introduce an innovative Inverted Virtual Screening (IVS) pipeline. This pipeline Integrated molecular dynamics and docking analyses to ensure that protein structures are not only energetically favorable but also representative of stable conformations. The primary objective of this pipeline is to automate and streamline the analysis of protein-ligand interactions at both genomic and transcriptomic scales. In the contemporary post-genomic era, high-throughput computational screening for bioproducts, biological systems, and therapeutic drugs has become a cornerstone practice. This approach offers the promise of cost-effectiveness, time efficiency, and optimization of laboratory work. Nevertheless, a notable deficiency persists in the availability of efficient pipelines capable of automating the virtual screening process, seamlessly integrating input and output, and leveraging the full potential of open-source tools. To bridge this critical gap, we have developed a versatile pipeline known as BioProtIS. This tool seamlessly integrates a suite of state-of-the-art tools, including Modeller, AlphaFold, Gromacs, FPOCKET, and AutoDock Vina, thus facilitating the streamlined docking of ligands with an expansive repertoire of proteins sourced from genomes and transcriptomes, and substrates. To assess the pipeline's performance, we employed the transcriptomes of Cereus jamacaru (a cactus species) and Aspisoma lineatum (firefly), along with the genome of Homo sapiens. This integration not only improves the accuracy of ligand-protein interactions by minimizing replicability deviations but also optimizes the discovery process by enabling the simultaneous evaluation of multiple substrates. Furthermore, our pipeline accommodates distinct testing scenarios, such as b

关键词： Inverted virtual screening Protein-ligand interactions Genomic exploration Bioproduct discovery bioinformatics integration

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Multi-Agent Based bioinformatics integration Using Distributed Dynamic Description Logics

Multi-Agent Based Bioinformatics Integration Using Distribut...

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5th International Conference on Semantics, Knowledge and Grid

作者： Wang, Zhuxiao Zhang, Dapeng Shi, Zhongzhi Chinese Acad Sci Grad Univ Key Lab Intelligent Informat Proc Inst Comp Technol Beijing Peoples R China Chinese Acad Sci Inst Comp Technol Key Lab Intelligent Informat Proc Beijing 100864 Peoples R China

ISBN: (纸本)9781424452781

integration of bioinformatics data repositories is a challenging task in which data sets are usually heterogeneous in structure and are often distributed across multiple, autonomously maintained databases. In this context, we present an innovative system which coordinates bioinformatics data by combining P2P data integration paradigm and Distributed Dynamic Description Logics (D3L) on top of Multi-Agent System infrastructure. We define the semantics and syntax of D3L, and propose a distributed consistency checking algorithm for realizing the intelligent query with logical reasoning function and decomposing large tasks to sub-tasks that could be tackled by different agents. Finally, we introduce a prototype implementation and present its evaluation. The results indicate that the proposed approach achieves excellent robustness and satisfactory performance.

关键词： bioinformatics integration agent technology Distributed Dynamic Description Logics

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Multi-Agent Based bioinformatics integration Using Distributed Dynamic Description Logics

Multi-Agent Based Bioinformatics Integration Using Distribut...

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Fifth International Conference on Semantics,Knowledge and Grid(第五届语义、知识与网格国际会议 SKG 2009)

作者： Zhuxiao Wang Dapeng Zhang Zhongzhi Shi Key Laboratory of Intelligent Information Processing Institute of Computing Technology Chinese Acad Key Laboratory of Intelligent Information Processing Institute of Computing Technology Chinese Acad

integration of bioinformatics data repositories is a challenging task in which data sets are usually heterogeneous in structure and are often distributed across multiple, autonomously maintained databases. In this context, we present an innovative system which coordinates bioinformatics data by combining P2P data integration paradigm and Distributed Dynamic Description Logics (D3L) on top of Multi- Agent System infrastructure. We define the semantics and syntax of D3L, and propose a distributed consistency checking algorithm for realizing the intelligent query with logical reasoning function and decomposing large tasks to sub-tasks that could be tackled by different agents. Finally, we introduce a prototype implementation and present its evaluation. The results indicate that the proposed approach achieves excellent robustness and satisfactory performance.

关键词： bioinformatics integration agent technology Distributed Dynamic Description Logics

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