Nanobiotechnology

Nanotıp: Moleküler Modelleme
Nanomedicine:Molecular Modelling
Tuğba Arzu ÖZAL İLDENİZa
aAcıbadem Mehmet Ali Aydınlar Üniversitesi Mühendislik Fakültesi, Tıp Mühendisliği Bölümü, İstanbul, TÜRKİYE
Özal İldeniz TA. Nanotıp: Moleküler modelleme. Akın A, editör. Nanobiyoteknoloji. 1. Baskı. Ankara: Türkiye Klinikleri; 2021. p.6-12.
Article Language: TR
ÖZET
Günümüzde bilgisayar teknolojilerinin her geçen gün ilerlemesiyle birlikte bilgisayar ortamında hesaplamalı olarak uygulanan moleküler modelleme yöntemleri de giderek daha da önem taşımaya başladı. Özellikle tedavi amaçlı kullanılan biyomoleküllerin vücut içerisindeki çalışma mekanizmalarının anlaşılması için kullanılan bu hesaplamalı yöntemler ilaç tasarımı alanında da büyük önem kazandı. Bir ilaç molekülünün tasarlanmasından piyasaya sürülmesine kadar olan süreçte bir çok faz çalışması yapılmaktadır. Moleküler modelleme yöntemleri bu sürecin kısalmasına olasılık sağlayarak maliyetin azalmasını sağlamaktadır. Moleküler modelleme yöntemlerinden en çok kullanılanları moleküler dinamik ve moleküler doklama yöntemleridir. Bunların yanı sıra matematiksel ifadelerin bilimsel kurallarla harmanlanması ile birçok değişik modelleme yöntemi uygulanmaktadır. Bu yöntemlerde 2 veya 3 boyutlu benzerlik çalışmalarının yanı sıra enerji uzayının taranmasına dayalı yöntemlerde bulunmaktadır. Son olarak yapay zeka yöntemlerinin uygulanması ile protein yapıdaki biyomoleküllerin 3 boyutlu yapılarının tahmini ilaç tasarımı alanında önemli bir adım olarak yerini almıştır.

Anahtar Kelimeler: Moleküler dinamik simülasyon; ilaç dizaynı; bilgisayar yardımlı tasarım
ABSTRACT
Recently with the improvements in computer technologies, molecular modelling techniques applied computationally in silico becomes more important. The computational methodolodies used especially to understand the working mechanisms of the biomolecules in the body that are utilized for therapeutic purposes. There are many phase studies for a drug molecule passing from the design till entering the market. Molecular modelling techniques enables shortenning of this period and resulting in the reduce of the cost. The most widely applied molecular modelling methologies are molecular dynamics and docking. Besides these, many different modelling techniques can be applied together with the combination of the mathematical formulas with scientific rules. Among these in addition to 2 or 3 dimensional homology modelling, there exists methodologies based on scanning the energy space. Lastly, prediction of structures of the biomolecules that are protein in nature with the application of artificial intelligance methodologies takes an important place in drug design.

Keywords: Molecular dynamics dimulation; drug design; computer-aided design

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