Podpora za grafične pospeševalnike v orodju za molekulsko sidranje

diplomsko delo

Miha Kovač (Author), Nejc Ilc (Mentor), Davor Sluga (Co-mentor)

Abstract

CmDock je odprtokodni program za simulacijo molekulskega sidranja. S pomočjo genetskega algoritma išče optimalno konformacijo manjše molekule, vezane na površino beljakovine. Program smo razširili z dvema izvedbama nove cenilne funkcije na osnovi odsekoma linearnega potenciala. Prva se izvaja na enem jedru centralne procesorske enote, druga pa izkorišča zmožnost vzporednega računanja na grafičnih pospeševalnikih in gradi na prototipu v ogrodju OpenCL. Rezultate nove cenilne funkcije smo primerjali z rezultati obstoječe, pri čemer smo ocenjevali točnost ter hitrost izračuna na treh izbranih testnih kompleksih. Pri enem izmed njih je rezultat bolj točen, pri ostalih dveh pa zaostajamo za obstoječo cenilno funkcijo. Izvajanje programa je z novo cenilno funkcijo na grafičnem pospeševalniku 3-krat hitrejše kot na centralni procesorski enoti ter 8-krat hitrejše kot z obstoječo cenilno funkcijo. Del, ki se v celoti izvede vzporedno, porabi na grafičnem pospeševalniku do 76-krat manj časa.

Keywords

molekulsko sidranje;CmDock;grafični pospeševalniki;OpenCL;C++;interdisciplinarni študij;univerzitetni študij;diplomske naloge;

Data

Language:	Slovenian
Year of publishing:	2023
Typology:	2.11 - Undergraduate Thesis
Organization:	UL FRI - Faculty of Computer and Information Science
Publisher:	[M. Kovač]
UDC:	004(043.2)
COBISS:	147351043
Views:	360
Downloads:	98
Average score:	0 (0 votes)
Metadata:

Other data

Secondary language:	English
Secondary title:	GPU support in molecular docking software
Secondary abstract:	CmDock is an open-source program intended for simulating molecular docking. It leverages a genetic algorithm to search for the optimal conformation of a small molecule (ligand) docked onto the surface of a protein. This thesis presents an improvement to the mentioned program by implementing two versions of a scoring function based on piecewise linear potential. The first one executes on the central processing unit (CPU), while the second one utilizes parallel computation capabilities of graphics processing units (GPUs) and is based on a prototype in OpenCL. We have compared the results of both versions; we evaluated the accuracy and speed on three protein-ligand complexes. Compared to the established scoring function, we achieved better accuracy when docking onto one of the three proteins, while docking on the other two was less successful. CmDock utilizing GPU accelerated scoring function achieves around 3x speedup over the equivalent CPU-based version and is around 8x faster than the existing version. Inspecting only the fully parallelizable part, we have observed up to 76x reduction in computation time when using GPU acceleration.
Secondary keywords:	molecular docking;CmDock;GPU;OpenCL;C++;computer science;computer and information science;computer science and mathematics;interdisciplinary studies;diploma;
Type (COBISS):	Bachelor thesis/paper
Study programme:	1000407
Embargo end date (OpenAIRE):	1970-01-01
Thesis comment:	Univ. v Ljubljani, Fak. za računalništvo in informatiko
Pages:	65 str.
ID:	18347636