Editing Protein tertiary structure (section)

== Projects ==

=== Prediction algorithm ===
The [[Folding@home]] project at the [[University of Pennsylvania]] is a [[distributed computing]] research effort which uses approximately 5 [[petaFLOPS]] (≈10 x86 petaFLOPS) of available computing. It aims to find an [[algorithm]] which will consistently predict protein tertiary and quaternary structures given the protein's amino acid sequence and its cellular conditions.<ref>{{Cite web |title=Folding@home – Fighting disease with a world wide distributed super computer. |url=https://foldingathome.org/ |access-date=2024-04-23 |language=en-US}}</ref><ref>{{Cite web |title=Bowman Lab – University of Pennsylvania |url=https://bowmanlab.seas.upenn.edu/ |access-date=2024-04-23 |language=en-US}}</ref>

A list of software for protein tertiary structure prediction can be found at
[[List of protein structure prediction software]].

=== Protein aggregation diseases ===
[[Protein aggregation]] diseases such as [[Alzheimer's disease]] and [[Huntington's disease]] and [[prion]] diseases such as [[bovine spongiform encephalopathy]] can be better understood by constructing (and reconstructing) [[disease model]]s. This is done by causing the disease in laboratory animals, for example, by administering a [[toxin]], such as [[MPTP]] to cause Parkinson's disease, or through [[genetic engineering|genetic manipulation]].<ref name="park">{{cite journal|title=Classic toxin-induced animal models of Parkinson's disease: 6-OHDA and MPTP|pmid=15503155|doi=10.1007/s00441-004-0938-y | volume=318|issue=1|date=October 2004|journal=Cell Tissue Res.|pages=215–24|author=Schober A|s2cid=1824912}}</ref><ref name="ko">{{cite web|url=http://www.sigmaaldrich.com/catalog/genes/TP53|title=Tp53 Knockout Rat|publisher=Cancer|access-date=2010-12-18}}</ref>
[[Protein structure prediction]] is a new way to create disease models, which may avoid the use of animals.<ref name="bit">{{cite web|url=http://www.bit-tech.net/hardware/graphics/2009/06/15/what-is-folding-and-why-does-it-matter/|title=Feature – What is Folding and Why Does it Matter?|access-date=December 18, 2010|archive-url=https://web.archive.org/web/20131212083942/http://www.bit-tech.net/hardware/graphics/2009/06/15/what-is-folding-and-why-does-it-matter/|archive-date=December 12, 2013|url-status=dead}}</ref>

===Protein Tertiary Structure Retrieval Project (CoMOGrad)===

Matching patterns in tertiary structure of a given protein to huge number of known protein tertiary structures and retrieve most similar ones in ranked order is in the heart of many research areas like function prediction of novel proteins, study of evolution, disease diagnosis, drug discovery, antibody design etc. The CoMOGrad project at BUET is a research effort to device an extremely fast and much precise method for protein tertiary structure retrieval and develop online tool based on research outcome.<ref>{{Cite web | url=http://research.buet.ac.bd:8080/Comograd/ |title = Comograd :: Protein Tertiary Matching}}</ref><ref>{{cite journal |last1=Karim |first1=Rezaul |last2=Aziz |first2=Mohd Momin Al |last3=Shatabda |first3=Swakkhar |last4=Rahman |first4=M. Sohel |last5=Mia |first5=Md Abul Kashem |last6=Zaman |first6=Farhana |last7=Rakin |first7=Salman |title=CoMOGrad and PHOG: From Computer Vision to Fast and Accurate Protein Tertiary Structure Retrieval |journal=Scientific Reports |date=21 August 2015 |volume=5 |issue=1 |pages=13275 |doi=10.1038/srep13275 |pmid=26293226 |pmc=4543952 |arxiv=1409.0814 |bibcode=2015NatSR...513275K }}</ref>