Markov state models

Link roundup: Apr–Jun 2021

less than 1 minute read

Published: June 30, 2021

Papers
Artificial intelligence in drug discovery: what is realistic, what are illusions? Part 1: Ways to make an impact, and why we are not there yet
Deep Dive into Machine Learning Models for Protein Engineering

Science
Kati Kariko Helped Shield the World From the Coronavirus
Six lessons from the biotech startup world

Others Scikit-learn Crash Course - Machine Learning Library for Python

Have you ever thought of the perfect quip or comeback after it didn’t matter—a minute, hour, or day after your conversation has ended?
Well, there’s a name for that phenomenon. It’s called l’esprit de l’escalier, or the spirit of the staircase, and refers to the perfect retort that arises at the wrong time.
– The Secret to Being Witty, Revealed

Link roundup: Jan–Mar 2021

1 minute read

Published: March 30, 2021

Papers
PLoS Comp Bio | Ten simple rules for quick and dirty scientific programming
Modern Phys Lett B | Current computational methods for enzyme design
Mol Cell | Computationally reconstructing cotranscriptional RNA folding from experimental data reveals rearrangement of non-native folding intermediates
J Chem Inf Model | Informatics for Chemistry, Biology, and Biomedical Sciences
PLoS Comp Bio | Ten simple rules for typographically appealing scientific texts
PLoS Comp Bio | Ten quick tips for making things findable

Science
What data can’t do
In the Pipeline | The Problem with COVID-19 Clinical Trials
How the West Lost COVID
In the Pipeline | Dealing With the Literature
The Sputnik V Vaccine and Russia’s Race to Immunity
Exploring the Supply Chain of the Pfizer/BioNTech and Moderna COVID-19 vaccines
GitHub | enspara Another MSM Python library
In the Pipeline | Myths of Vaccine Manufacturing
NY Times | The Science of Reasoning With Unreasonable People
Nature | Explaining the icy mystery of the Dyatlov Pass deaths
‘But I never smoked’: A growing share of lung cancer cases is turning up in an unexpected population
How to be lucky
Nature | Ten computer codes that transformed science
Reverse Engineering the source code of the BioNTech/Pfizer SARS-CoV-2 Vaccine
The Atlantic | Where the Pandemic Will Take America in 2021

Others
Phantasia
The History of Philosophy From the Perspective of Chicken Enchiladas
Daniel Dennett’s Science of the Soul
Nature | Five tips for understanding and managing your emotions to build flourishing connections
INCIDENTAL COMICS | The hierarchy of needs
AMERICAN PSYCHOSIS - Chris Hedges
Stunning Images of Starlings in Flight
Some of Us Did Not Die
How to write a more compelling sentence
Dinosaur Comics | entropy wolf
SMBC | Science Fictions
SMBC | Think
Who Invented the Alphabet?
‘Kulning’: A hypnotic Swedish singing tradition
Language Log | Who created batik? Who appropriated batik?

2020 book list

1 minute read

Published: January 05, 2021

Hopefully in 2020 I will read even more!

Link roundup: Oct–Dec 2020

4 minute read

Published: December 31, 2020

The world came into a standstill in March, including this blog. Here’s to a restart.

Papers
Science | Genetic interaction mapping informs integrative structure determination of protein complexes
Chem Sci | Ligand design by targeting a binding site water
Sci. Rep | Statistics for the analysis of molecular dynamics simulations: providing P values for agonist-dependent GPCR activation
Science | Protein storytelling through physics Nice general MD review
J Med Chem | Chemists: AI Is Here; Unite To Get the Benefits
Sci. Rep | Moving targets in drug discovery

Science
In the Pipeline | The New Mutations
It occurred to me that I’m trying to introduce mutations to my enzyme and here is the virus doing just that using the world as its test tube…What do you call this? Poignant? Amusing? Ironic?
The Atlantic | How COVID-19 Changes Our Sleep
The Atlantic | How Science Beat the Virus
Nature | The peanut snack that triggered a fresh approach to allergy prevention
How the novel coronavirus has evolved
Nature | Oxford COVID vaccine paper highlights lingering unknowns about results
PyCaret: Useful ML tool for chemoinformatics #chemoinformatics #RDKit #Machine learning
Nature | How to write a superb literature review
In the Pipeline | Get Ready for False Side Effects
Sci Am | The COVID Science Wars
Helen Berman: the crystallographer who pioneered the Protein Data Bank
Nautilus | Kim Stanley Robinson Holds Out Hope
Nature | Postdoc survey reveals disenchantment with working life
‘disenchantment’ is a curious diction… I suppose many of us have been charmed by the wizards of the ivory tower.
Life with purpose
Nature | Why your scientific presentation should not be adapted from a journal article
COVID-19 Molecular Structure and Therapeutics Hub
In the Pipeline | Vaccine Possibilities
SciAm | Mysteries of COVID Smell Loss Finally Yield Some Answers
Nature | Five rules for evidence communication
meta, biomedical research search engine
Nature | Science search engine links papers to grants and patents
C&EN | Covalent drugs go from fringe field to fashionable endeavor
In the Pipeline | Vaccine Efficacy Data!
How can climate be predictable if weather is chaotic?
brainpickings | Tenacity, the Art of Integration, and the Key to a Flexible Mind: Wisdom from the Life of Mary Somerville, for Whom the Word “Scientist” Was Coined
The New Yorker | How the Coronavirus Hacks the Immune System

Others
Educated Fools: Why Democratic leaders still misunderstand the politics of social class
Beyond Tokyo and Jerusalem Shusaku Endo’s Silence review
Yo-Yo Ma, Kathryn Stott - Over the Rainbow (Official Video)
LARB | Of Course They Would: On Kim Stanley Robinson’s “The Ministry for the Future”
Thesis Whisperer | While you scream inside your heart, please keep working.
Do Elephants Have Souls?
Huawei, 5G, and the Man Who Conquered Noise
Wired | Remembrance
How to have a difficult conversation
Twitter magic realism bot
See a Stunningly Surreal Bookstore in China

Python
Top 11 Github Repositories to Learn Python
github.com/TomNicholas/Python-for-Scientists
github.com/garrettj403/SciencePlots
github.com/rasbt/python_reference
github.com/matplotlib/AnatomyOfMatplotlib
github.com/jerry-git/learn-python3

Do you need a little darkness to get you going? –Mary Oliver

He adopted the following strategy: say what you know; what you don’t know; what you are doing to find out; what people can do in the meantime to be on the safe side; and that advice will change –Nature article

In my work as a mediator, I’ve learnt that successful conversations always involve what I call a ‘gem statement’. When two parties have listened long and hard to each other – have made the heroic effort to listen curiously and empathically even when they disagree strenuously – someone eventually unearths a glowing, priceless gem. It usually takes the form of a short, powerful statement –How to have a difficult conversation

aside from faith,
as far as you know,
you will never have another heart.
better to grow the one you were born with.
–Anahata, by Lenelle Moïse