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tlnagy committed Dec 22, 2015
1 parent d5b6fe4 commit e83b44d14457b68ea6384542387e81408a2f33f5
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layout: post
title: Open
tags: oss
categories: blog
author: Tamas Nagy
---

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title: "Scholarly Markdown for Scientific Writing "
layout: post
tags: [science, writing, markdown]
categories: blog
author: Tamas Nagy
---
Scientific writing has come a long way since typewriters and stacks of handwritten reference cards. Robust reference managers, automatically generated bibliographies, and editable files are significant improvements.
@@ -3,7 +3,6 @@ title: Life, Sans Facebook
layout: post
author: Tamas Nagy
tags: [productivity, minimalism, social media]
categories: blog
---
It has been around three months since, after much back and forth in my head, I decided to permanently delete my Facebook account. In that time, I've been asked several times why I left, so I opted to write this short post to spell out my thoughts in a more succinct and thorough manner.

@@ -3,7 +3,6 @@ title: Predicting Drug Candidate Promiscuity
author: Tamas Nagy
layout: post
tags: [science, math]
categories: blog
---
Last month, I gave a presentation to my chemistry seminar class on predicting the promiscuity of small-molecule drug candidates by comparing their structure to the sets of ligands that bind specific proteins. If a drug candidate strongly matches a set of ligands for a certain protein then there is a high probability that it will show off-target effects with that protein. Thus, if a candidate is compared against enough protein-ligand sets then it is likely that we can predict the side-effects of a drug before it enters clinical trials. Using this technique, Keiser et al. were able to identify potential reasons for side effects seen in commonly available drugs [@keiser_predicting_2009]. For example, they noticed that Rescriptor, an HIV reverse transcriptase inhibitor, matched the ligand sets of histamine receptors, which could explain the skin rashes observed in patients who were on the drug. They used a variant of the [Jaccard index](http://en.wikipedia.org/wiki/Jaccard_index) known as the Tanimoto coefficient to calculate the similarity between pairs of compounds:

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