Vina-FPGA: A Hardware-Accelerated Molecular Docking Tool With Fixed-Point Quantization and Low-Level Parallelism

Ling, Ming; Lin, Qingde; Chen, Ruiqi; Qi, Haimeng; Lin, Mengru; Zhu, Yanxiang; Wu, Jiansheng

doi:10.1109/tvlsi.2022.3217275

Cited by 10 publications

(2 citation statements)

References 26 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…We employed AutoDock Vina docking, given the involvement of the catalytic pocket and the transport catalytic channel in the chitin synthesis process [ 52 ]. Perhaps some of the latest methods that other researchers have recently explored to improve on docking tools can be used, such as force field improvements, conformation search algorithm improvements, and scoring function improvements [ 53 , 54 , 55 , 56 , 57 , 58 , 59 , 60 , 61 , 62 , 63 ]. Within the catalytic pocket, residue D496 functions as the catalytic residue, facilitating nucleophilic addition via protonation, while residue E495 assists in substrate recognition and alignment [ 64 ].…”

Section: Discussionmentioning

confidence: 99%

Rationally Designed Novel Antimicrobial Peptides Targeting Chitin Synthase for Combating Soybean Phytophthora Blight

Ran,

Shehzadi,

Liang

et al. 2024

IJMS

View full text Add to dashboard Cite

Soybean phytophthora blight is a severe menace to global agriculture, causing annual losses surpassing USD 1 billion. Present crop loss mitigation strategies primarily rely on chemical pesticides and disease-resistant breeding, frequently surpassed by the pathogens’ quick adaptive evolution. In this urgent scenario, our research delves into innovative antimicrobial peptides characterized by low drug resistance and environmental friendliness. Inhibiting chitin synthase gene activity in Phytophthora sojae impairs vital functions such as growth and sporulation, presenting an effective method to reduce its pathogenic impact. In our study, we screened 16 previously tested peptides to evaluate their antimicrobial effects against Phytophthora using structure-guided drug design, which involves molecular docking, saturation mutagenesis, molecular dynamics, and toxicity prediction. The in silico analysis identified AMP_04 with potential inhibitory activity against Phytophthora sojae’s chitin synthase. Through three rounds of saturation mutagenesis, we pin-pointed the most effective triple mutant, TP (D10K, G11I, S14L). Molecular dynamic simulations revealed TP’s stability in the chitin synthase-TP complex and its transmembrane mechanism, employing an all-atom force field. Our findings demonstrate the efficacy of TP in occupying the substrate-binding pocket and translocation catalytic channel. Effective inhibition of the chitin synthase enzyme can be achieved. Specifically, the triple mutant demonstrates enhanced antimicrobial potency and decreased toxicity relative to the wild-type AMP_04, utilizing a mechanism akin to the barrel-stave model during membrane translocation. Collectively, our study provides a new strategy that could be used as a potent antimicrobial agent in combatting soybean blight, contributing to sustainable agricultural practices.

show abstract

Section: Discussionmentioning

confidence: 99%

Rationally Designed Novel Antimicrobial Peptides Targeting Chitin Synthase for Combating Soybean Phytophthora Blight

Ran,

Shehzadi,

Liang

et al. 2024

IJMS

View full text Add to dashboard Cite

show abstract

“…Although AutoDock Vina has good docking accuracy and speed, the long iterations and irregular nature of the algorithm make it difficult to deploy on hardware acceleration devices. However, Ming L et al [41] have proactively explored the available logical units for concurrent computation in the AutoDock Vina algorithm, such as parallel computation of intramolecular and intermolecular energy, updating of Hessian matrix involved in the BFGS algorithm, and a novel BRAM access strategy based on data rearrangement. When ensuring relative docking accuracy, the Vina-FPGA [41] version implemented by Ming L et al only consumes 2.5% of the energy consumed by the CPU version, and achieves an average speed-up ratio of 3.7 times.…”

Section: Intrinsically Concurrently Computable Logical Unitmentioning

confidence: 99%

A Review of the Parallelization Strategies for Iterative Algorithms

Zhou,

Ling,

Tang

et al. 2023

Preprint

Self Cite

View full text Add to dashboard Cite

Iteration-based algorithms have been widely used and achieved excellent results in many fields. However, in the big data era, data that needs to be processed is enormous in terms of both depth (the dimensionality of data) and breadth (the volume of data). Due to the slowdown of Moore's Law, the computing power of single-core CPUs is becoming saturated. The increase in the computational complexity and the bottleneck of the single-core processor’s speed exacerbate the time-consuming problem of iterative algorithms. With the rise of multi-core computers and distributed computing systems, parallelizing and deploying iterative algorithms on such systems can make full use of computing resources and accelerate iterative computation, providing a new idea for solving the aforementioned problems. However, due to the logical dependency between two consecutive iterations in an iterative algorithm, it is difficult to directly implement the concurrent computation of such algorithms. To this end, many studies have been conducted on the parallelization of iterative algorithms in both academia and industry. This paper aims to conduct an in-depth research and analysis of these parallelization strategies. Firstly, the abstract description and classification of iterative algorithms are given. Then four concurrency strategies for iterative algorithms are summarized, including logical units that can be intrinsically concurrently computed, multi-initial state parallel search strategy, data parallelism, and task parallelism. Finally, the paper detailed the convergence of parallel iterative algorithms, focusing on building the mathematical model of asynchronous iterative algorithms, and summarizing the convergence conditions of asynchronous iterative algorithms.

show abstract

T5S1607 identified as a antibacterial FtsZ inhibitor：Virtual screening combined with bioactivity evaluation for the drug discovery

Xie,

Ruan,

Guo

et al. 2024

Computational Biology and Chemistry

View full text Add to dashboard Cite

Vina-FPGA: A Hardware-Accelerated Molecular Docking Tool With Fixed-Point Quantization and Low-Level Parallelism

Cited by 10 publications

References 26 publications

Rationally Designed Novel Antimicrobial Peptides Targeting Chitin Synthase for Combating Soybean Phytophthora Blight

Rationally Designed Novel Antimicrobial Peptides Targeting Chitin Synthase for Combating Soybean Phytophthora Blight

A Review of the Parallelization Strategies for Iterative Algorithms

T5S1607 identified as a antibacterial FtsZ inhibitor：Virtual screening combined with bioactivity evaluation for the drug discovery

Contact Info

Product

Resources

About