AlphaFold 2 Paper with Code

Key Takeaways

so late last year there was an announcement that alpha photo2 could rival experimental results of the x-ray crystallography in predicting the protein structure accurately and at the time of the launch of the news the source code and also the research paper describing part two of alpha fold was not yet released and so two days ago on july 15 the team behind alpha photo just published their own work in the nature journal and the code that will allow you to reproduce the experimental prediction is provided on github and so in this video i'm going to show you the code and also the paper as well as providing you an overview of what is alpha photo 2 all about and so let's dive in so as mentioned already news about the alpha photo on its rival of the x-ray crystallography in predicting the protein structure accurately the news was released in november of 2020 and so this is the news and i'll provide you the links to this blog post and it does a very good job in summarizing the high level concept of what is protein structure and why do we need to predict it and so in a nutshell proteins are the powerhouses of the cell and they are essential for sustaining life and there are more than 30 000 proteins in human body performing various functions for example hemoglobin which transports oxygen that we intake to the tissue we have several enzymes performing various catalytic activity that help us to break down food to energy help with energy intake as well as all of the minute detail that sustained life and so the ability to take a amino acid sequence and then make a prediction as to the three-dimensional structure will provide biochemists and biologists the fundamental background that will help them to design better drugs understand the protein activity that they could use in order to develop more enhanced drugs as well as helping us to combat various diseases and so let's take a quick look here so you could definitely check out this two-minute video that explains the protein folding so as i mentioned already we're going from a basic amino acid sequence which could be thought of as kind of like a thread and then you're going to fold the thread in three dimension but then the thing is how do you exactly fold the thread into a three dimension and so that is where alpha photo will come in it will take a thread which is a linear thread and it will fold it into a three-dimensional shape that will resemble the actual protein structure that we could figure out traditionally by performing x-ray crystallography okay so let's jump back in to the github and so this is the github of alpha 4.2 and so all of the code are packaged inside the docker container and so you could have a look here in green it is the experimental results and in blue here it is the computational prediction from the alpha fold to and so it received a mark greater than 90 gdt which is an indicator of its accuracy and so you can see that both protein structure when you take both of them and then you align them by superimposing on one another they provide roughly almost a perfect fit and so this is the instruction for you to run your own copy of the alpha photo ii so you will need a docker container and then you'll probably have to install the nvidia container toolkit as well and for that you could follow the instructions provided here and another point you notice that you will also have to download all of the databases that are prerequisite for the apple photo too and so all of this could be downloaded from their custom script and so it will take about 8 to 12 hours and note that when you download it it will be 428 gigabytes but then when you unpacked it it will be almost 2.2 terabytes of space so make sure to have apple amount of storage in order to proceed further and you would follow all of the instructions here they're providing the model parameters for you to use as well and they provide you the commands that you could use to run the alpha fold and so they have already tested this on the nvidia gpu cloud image which contains 12 virtual cpu 85 gigabytes of ram 100 gigabytes of boot disk as well as three terabyte of storage and they use the a100 gpu so you can follow the instructions here in order to install and run the docker version of the alpha fold and so after running the calculation you will get the output and then the output will be described here and then you're going to see that there are quite a few files generated and so they even have the features the pickled version of it which produces the structure and then the pdb is a protein databank file format for depicting the three-dimensional shape of the protein structure and so you will need a viewer such as the pimo software in order to visualize the three-dimensional structure of the predicted protein structure all right and then you could definitely check out the other descriptions provided here and in this section they mentioned that because the databases are continuously changing and updating therefore the prediction that you will get might be a bit different from what they have got from their computation in the cache and so they mentioned that if you would like to get the same exact prediction you would have to use the same exact database version number which they provided here and if you're making use of the code that they provide on the github you should definitely cite their work which is published in nature which is right here and so you can see here that it is published on july 15th and the title of the paper is highly accurate protein structure prediction with alpha fold and so there is a pdf version of the article which you could click on and you might have already noticed that the article is not yet published in full form so it is provided as a preview and so you can check out the details of the inner workings of the apple photo 2 and so conceptually you can see here that is based on the transformer called evolved former and they even provided you with this schematic diagram let me show you right here of the prediction of how they started from the input protein sequence and then they generated the msa and then they used that as input for the evil former in order to get the structure modules and then eventually they got the protein structure prediction okay and so that is a quick overview of the alpha photo 2 and the corresponding code on github and i'll provide you the links of all of these in the video description and if you haven't already make sure to check out the prior videos that i have made on alpha 4.2 and so please find the link up above and if you find value in the video please support the channel by smashing the like button subscribing if you haven't already and also make sure to hit on the notification bell so that you will be notified of the next video and as always the best way to learn data science is to do data science and please enjoy the journey