PMID- 37828771
OWN - NLM
STAT- MEDLINE
DCOM- 20231101
LR  - 20231101
IS  - 1875-6697 (Electronic)
IS  - 1573-4099 (Linking)
VI  - 20
IP  - 3
DP  - 2024
TI  - A New Optimized Hybridization Approach for in silico High Throughput Molecular 
      Docking on FPGA Platform.
PG  - 236-247
LID - 10.2174/1573409919666230503094411 [doi]
AB  - BACKGROUND: The development process of a new drug should be a subject of 
      continuous evolution and rapid improvement as drugs are essential to treat a wide 
      range of diseases of which many are life-threatening. The advances in technology 
      resulted in a novel track in drug discovery and development known as in silico 
      drug design. The molecular docking phase plays a vital role in in silico drug 
      development process. In this phase, thousands of 3D conformations of both the 
      ligand and receptor are generated and the best conformations that create the most 
      stable drug-receptor complex are determined. The speed in finding accurate and 
      high-quality complexes depends on the efficiency of the search function in the 
      molecular docking procedure. OBJECTIVE: The objective of this research is to 
      propose and implement a novel hybrid approach called hABCDE to replace the EMC 
      searching part inside the BUDE docking algorithm. This helps in reaching the best 
      solution in a much accelerated time and higher solution quality compared to using 
      the ABC and DE algorithms separately. METHODS: In this work, we have employed a 
      new approach of hybridization between the Artificial Bee Colony (ABC) algorithm 
      and the Differential Evolution (DE) algorithm as an alternative searching part of 
      the Bristol University Docking Engine (BUDE) in order to accelerate the search 
      for higher quality solutions. Moreover, the proposed docking approach was 
      implemented on Field Programmable Gate Array (FPGA) parallel platform using 
      Vivado High-Level Synthesis Tool (HLST) in order to optimize and enhance the 
      execution time and overall efficiency. The NDM-1 protein was used as a model 
      receptor in our experiments to demonstrate the efficiency of our approach. 
      RESULTS: The NDM-1 protein was used as a model receptor in our experiments to 
      demonstrate the efficiency of our approach. The results showed that the execution 
      time for the BUDE with the new proposed hybridization approach was improved by 
      9,236 times. CONCLUSION: Our novel approach was significantly effective to 
      improve the functionality of docking algorithms (Bristol University Docking 
      Engine (BUDE)).
CI  - Copyright(c) Bentham Science Publishers; For any queries, please email at 
      epub@benthamscience.net.
FAU - Jarrah, Amin
AU  - Jarrah A
AD  - Department of Computer Engineering, Hijjawi Faculty for Engineering Technology, 
      Yarmouk University, Irbid, 21163, Jordan.
FAU - Lababneh, Jawad
AU  - Lababneh J
AD  - Department of Computer Engineering, Hijjawi Faculty for Engineering Technology, 
      Yarmouk University, Irbid, 21163, Jordan.
LA  - eng
PT  - Journal Article
PL  - United Arab Emirates
TA  - Curr Comput Aided Drug Des
JT  - Current computer-aided drug design
JID - 101265750
RN  - 0 (Proteins)
SB  - IM
MH  - Humans
MH  - Molecular Docking Simulation
MH  - *Algorithms
MH  - *Proteins/metabolism
MH  - Drug Design
OTO - NOTNLM
OT  - BUDE
OT  - FPGA
OT  - Molecular docking
OT  - artificial bee colony algorithm
OT  - differential evolution algorithm
OT  - optimization
OT  - parallel processing
OT  - vivado HLS
EDAT- 2023/10/13 06:45
MHDA- 2023/11/01 12:45
CRDT- 2023/10/13 02:58
PHST- 2022/09/29 00:00 [received]
PHST- 2023/03/19 00:00 [revised]
PHST- 2023/03/21 00:00 [accepted]
PHST- 2023/11/01 12:45 [medline]
PHST- 2023/10/13 06:45 [pubmed]
PHST- 2023/10/13 02:58 [entrez]
AID - CAD-EPUB-131416 [pii]
AID - 10.2174/1573409919666230503094411 [doi]
PST - ppublish
SO  - Curr Comput Aided Drug Des. 2024;20(3):236-247. doi: 
      10.2174/1573409919666230503094411.