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Dimorphite-DL and biotite-tools, two open source programs for the acceleration of structure-based drug design

Kaminsky, Jesse C. (2019) Dimorphite-DL and biotite-tools, two open source programs for the acceleration of structure-based drug design. Undergraduate Thesis, University of Pittsburgh. (Unpublished)

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Computer-aided drug design has seen a proliferation of tools that allow the manipulation
of small molecule and macromolecular structures in increasingly high-throughput settings.
Molecular dynamics simulations, small molecule docking software, and visualization tools allow
researchers to rapidly identify drug candidates and narrow the list of compounds that
experimentalists must consider for further testing. Any gap in automating computer-aided drug
design thus delays potentially life-saving discoveries. Here we present two open-source programs
we developed to address challenges facing both protein and ligand preparation. Dimorphite-DL
is a lightweight python program that predicts protonation states of small molecules using an
empirical approach to ensure accurate docking and modelling calculations. The presence or
absence of a hydrogen atom often determines whether a given ligand will bind a protein of interest.
Biotite-tools is a python package that provides several popular statistical functions for analyzing
molecular dynamics simulations in an easy-to-use way. Conformational fluctuation is complex,
and it can be challenging to extract insight from what is essentially a “protein movie.” As such,
simulation analysis has largely been restricted to those with backgrounds in computation, limiting
the scope of such a powerful tool. Biotite-tools aims to accelerate the efforts of those already
working with molecular dynamics and make analysis more accessible to experimentalists.


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Item Type: University of Pittsburgh ETD
Status: Unpublished
CreatorsEmailPitt UsernameORCID
Kaminsky, Jesse C.JCK69@pitt.edujck690000-0001-5796-2874
ETD Committee:
TitleMemberEmail AddressPitt UsernameORCID
Committee ChairDurrant, Jacobdurrantj
Committee MemberGorfe, Alemayehu
Committee MemberBerman, Andreaajb190
Committee MemberChong, Lillianltchong
Date: 15 April 2019
Date Type: Publication
Defense Date: 28 March 2019
Approval Date: 15 April 2019
Submission Date: 11 April 2019
Access Restriction: No restriction; Release the ETD for access worldwide immediately.
Number of Pages: 41
Institution: University of Pittsburgh
Schools and Programs: David C. Frederick Honors College
Degree: BPhil - Bachelor of Philosophy
Thesis Type: Undergraduate Thesis
Refereed: Yes
Uncontrolled Keywords: Molecular Dynamics, Cheminformatics, Bioinformatics, Biomedical Tool Development, Open Source
Date Deposited: 15 Apr 2019 18:30
Last Modified: 15 Apr 2019 18:30


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