AlphaFold

AlphaFold is an artificial intelligence (AI) program developed by DeepMind, a subsidiary of Alphabet,

which performs predictions of protein structure.[1] The program is designed as a deep learning system.[2]

AlphaFold software has had three major versions. A team of researchers that used AlphaFold 1 (2018)
placed first in the overall rankings of the 13th Critical Assessment of Structure Prediction (CASP) in
December 2018. The program was particularly successful at predicting the most accurate structure for
targets rated as the most difficult by the competition organisers, where no existing template structures
were available from proteins with a partially similar sequence. A team that used AlphaFold 2 (2020)
repeated the placement in the CASP14 competition in November 2020.[3] The team achieved a level of
accuracy much higher than any other group.[2][4] It scored above 90 for around two-thirds of the proteins
in CASP's global distance test (GDT), a test that measures the degree to which a computational program
predicted structure is similar to the lab experiment determined structure, with 100 being a complete
match, within the distance cutoff used for calculating GDT.[2][5]

AlphaFold 2's results at CASP14 were described as "astounding"[6] and "transformational".[7] Some
researchers noted that the accuracy is not high enough for a third of its predictions, and that it does not
reveal the mechanism or rules of protein folding for the protein folding problem to be considered
solved.[8][9] Nevertheless, there has been widespread respect for the technical achievement. On 15 July
2021 the AlphaFold 2 paper was published in Nature as an advance access publication alongside open
source software and a searchable database of species proteomes.[10][11][12] The paper has since been cited
more than 27 thousand times.

AlphaFold 3 was announced on 8 May 2024. It can predict the structure of complexes created by proteins
with DNA, RNA, various ligands, and ions.[13] The new prediction method shows a minimum 50%
improvement in accuracy for protein interactions with other molecules compared to existing methods.
Moreover, for certain key categories of interactions, the prediction accuracy has effectively doubled.[14]
Demis Hassabis and John Jumper from the team that developed AlphaFold won the Nobel Prize in
Chemistry in 2024 for their work on “protein structure prediction”. The two had won the Breakthrough
Prize in Life Sciences and the Albert Lasker Award for Basic Medical Research earlier in 2023.[15][16]

Background
Proteins consist of chains of amino acids which spontaneously fold to form the three dimensional (3-D)
structures of the proteins. The 3-D structure is crucial to understanding the biological function of the
protein.

Protein structures can be determined experimentally through techniques such as X-ray crystallography,
cryo-electron microscopy and nuclear magnetic resonance, which are all expensive and time-
consuming.[17] Such efforts, using the experimental methods, have identified the structures of about
170,000 proteins over the last 60 years, while there are over 200 million known proteins across all life
forms.[5]
Over the years, researchers have applied numerous
computational methods to predict the 3D structures of
proteins from their amino acid sequences, accuracy of
such methods in best possible scenario is close to
experimental techniques (NMR) by the use of
homology modeling based on molecular evolution.
CASP, which was launched in 1994 to challenge the
scientific community to produce their best protein
structure predictions, found that GDT scores of only
about 40 out of 100 can be achieved for the most
difficult proteins by 2016.[5] AlphaFold started
competing in the 2018 CASP using an artificial
intelligence (AI) deep learning technique.[17]

Algorithm
DeepMind is known to have trained the program on Amino-acid chains, known as polypeptides, fold to
over 170,000 proteins from the Protein Data Bank, a form a protein.
public repository of protein sequences and structures.
The program uses a form of attention network, a deep
learning technique that focuses on having the AI identify parts of a larger problem, then piece it together
to obtain the overall solution.[2] The overall training was conducted on processing power between 100
and 200 GPUs.[2]

AlphaFold 1 (2018)

AlphaFold 1 (2018) was built on work developed by various teams in the 2010s, work that looked at the
large databanks of related DNA sequences now available from many different organisms (most without
known 3D structures), to try to find changes at different residues that appeared to be correlated, even
though the residues were not consecutive in the main chain. Such correlations suggest that the residues
may be close to each other physically, even though not close in the sequence, allowing a contact map to
be estimated. Building on recent work prior to 2018, AlphaFold 1 extended this to estimate a probability
distribution for just how close the residues might be likely to be—turning the contact map into a likely
distance map. It also used more advanced learning methods than previously to develop the
inference.[18][19]

AlphaFold 2 (2020)

The 2020 version of the program (AlphaFold 2, 2020) is significantly different from the original version
that won CASP 13 in 2018, according to the team at DeepMind.[21][22]

The software design used in AlphaFold 1 contained a number of modules, each trained separately, that
were used to produce the guide potential that was then combined with the physics-based energy potential.
AlphaFold 2 replaced this with a system of sub-networks coupled together into a single differentiable
end-to-end model, based entirely on pattern recognition, which was trained in an integrated way as a
single integrated structure.[22][23] Local physics, in the
form of energy refinement based on the AMBER
model, is applied only as a final refinement step once
the neural network prediction has converged, and only
slightly adjusts the predicted structure.[24]

A key part of the 2020 system are two modules,

believed to be based on a transformer design, which are
used to progressively refine a vector of information for
each relationship (or "edge" in graph-theory
AlphaFold 2 performance, experiments, and
terminology) between an amino acid residue of the
architecture[20]
protein and another amino acid residue (these
relationships are represented by the array shown in
green); and between each amino acid position and each
different sequences in the input sequence alignment
(these relationships are represented by the array shown
in red).[23] Internally these refinement transformations
contain layers that have the effect of bringing relevant
data together and filtering out irrelevant data (the
"attention mechanism") for these relationships, in a
context-dependent way, learnt from training data. These
transformations are iterated, the updated information
output by one step becoming the input of the next, with
the sharpened residue/residue information feeding into
Architectural details of AlphaFold 2[20]
the update of the residue/sequence information, and
then the improved residue/sequence information
feeding into the update of the residue/residue information.[23] As the iteration progresses, according to
one report, the "attention algorithm ... mimics the way a person might assemble a jigsaw puzzle: first
connecting pieces in small clumps—in this case clusters of amino acids—and then searching for ways to
join the clumps in a larger whole."[5]

The output of these iterations then informs the final structure prediction module,[23] which also uses
transformers,[25] and is itself then iterated. In an example presented by DeepMind, the structure
prediction module achieved a correct topology for the target protein on its first iteration, scored as having
a GDT_TS of 78, but with a large number (90%) of stereochemical violations – i.e. unphysical bond
angles or lengths. With subsequent iterations the number of stereochemical violations fell. By the third
iteration the GDT_TS of the prediction was approaching 90, and by the eighth iteration the number of
stereochemical violations was approaching zero.[26]

The training data was originally restricted to single peptide chains. However, the October 2021 update,
named AlphaFold-Multimer, included protein complexes in its training data. DeepMind stated this update
succeeded about 70% of the time at accurately predicting protein-protein interactions.[27]

AlphaFold 3 (2024)
Announced on 8 May 2024, AlphaFold 3 was co-developed by Google DeepMind and Isomorphic Labs,
both subsidiaries of Alphabet. AlphaFold 3 is not limited to single-chain proteins, as it can also predict
the structures of protein complexes with DNA, RNA, post-translational modifications and selected
ligands and ions.[28][13]

AlphaFold 3 introduces the "Pairformer", a deep learning architecture inspired from the transformer,
considered similar but simpler than the Evoformer introduced with AlphaFold 2.[29][30] The raw
predictions from the Pairformer module are passed to a diffusion model, which starts with a cloud of
atoms and uses these predictions to iteratively progress towards a 3D depiction of the molecular
structure.[13]

The AlphaFold server was created to provide free access to AlphaFold 3 for non-commercial research.[31]

Competitions

CASP13

Results achieved for protein prediction by the best reconstructions in the CASP
2018 competition (small circles) and CASP 2020 competition (large circles),
compared with results achieved in previous years.
The crimson trend-line shows how a handful of models including AlphaFold 1
achieved a significant step-change in 2018 over the rate of progress that had
previously been achieved, particularly in respect of the protein sequences
considered the most difficult to predict.
(Qualitative improvement had been made in earlier years, but it is only as changes
bring structures within 8 Å of their experimental positions that they start to affect the
CASP GDS-TS measure).
The orange trend-line shows that by 2020 online prediction servers had been able
to learn from and match this performance, while the best other groups (green curve)
had on average been able to make some improvements on it. However, the black
trend curve shows the degree to which AlphaFold 2 had surpassed this again in
2020, across the board.
The detailed spread of data points indicates the degree of consistency or variation
achieved by AlphaFold. Outliers represent the handful of sequences for which it did
not make such a successful prediction.
In December 2018, DeepMind's AlphaFold placed first in the overall rankings of the 13th Critical
Assessment of Techniques for Protein Structure Prediction (CASP).[32][33]

The program was particularly successfully predicting the most accurate structure for targets rated as the
most difficult by the competition organisers, where no existing template structures were available from
proteins with a partially similar sequence. AlphaFold gave the best prediction for 25 out of 43 protein
targets in this class,[33][34][35] achieving a median score of 58.9 on the CASP's global distance test (GDT)
score, ahead of 52.5 and 52.4 by the two next best-placed teams,[36] who were also using deep learning to
estimate contact distances.[37][38] Overall, across all targets, the program achieved a GDT score of
68.5.[39]

In January 2020, implementations and illustrative code of AlphaFold 1 was released open-source on
GitHub.[40][17] but, as stated in the "Read Me" file on that website: "This code can't be used to predict
structure of an arbitrary protein sequence. It can be used to predict structure only on the CASP13 dataset
(links below). The feature generation code is tightly coupled to our internal infrastructure as well as
external tools, hence we are unable to open-source it." Therefore, in essence, the code deposited is not
suitable for general use but only for the CASP13 proteins. The company has not announced plans to make
their code publicly available as of 5 March 2021.

CASP14
In November 2020, DeepMind's new version, AlphaFold 2, won CASP14.[41][42] Overall, AlphaFold 2
made the best prediction for 88 out of the 97 targets.[6]

On the competition's preferred global distance test (GDT) measure of accuracy, the program achieved a
median score of 92.4 (out of 100), meaning that more than half of its predictions were scored at better
than 92.4% for having their atoms in more-or-less the right place,[43][44] a level of accuracy reported to be
comparable to experimental techniques like X-ray crystallography.[21][7][39] In 2018 AlphaFold 1 had
only reached this level of accuracy in two of all of its predictions.[6] 88% of predictions in the 2020
competition had a GDT_TS score of more than 80. On the group of targets classed as the most difficult,
AlphaFold 2 achieved a median score of 87.

Measured by the root-mean-square deviation (RMS-D) of the placement of the alpha-carbon atoms of the
protein backbone chain, which tends to be dominated by the performance of the worst-fitted outliers, 88%
of AlphaFold 2's predictions had an RMS deviation of less than 4 Å for the set of overlapped C-alpha
atoms.[6] 76% of predictions achieved better than 3 Å, and 46% had a C-alpha atom RMS accuracy better
than 2 Å,[6] with a median RMS deviation in its predictions of 2.1 Å for a set of overlapped CA atoms.[6]
AlphaFold 2 also achieved an accuracy in modelling surface side chains described as "really really
extraordinary".

To additionally verify AlphaFold-2 the conference organisers approached four leading experimental
groups for structures they were finding particularly challenging and had been unable to determine. In all
four cases the three-dimensional models produced by AlphaFold 2 were sufficiently accurate to determine
structures of these proteins by molecular replacement. These included target T1100 (Af1503), a small
membrane protein studied by experimentalists for ten years.[5]
Of the three structures that AlphaFold 2 had the least success in predicting, two had been obtained by
protein NMR methods, which define protein structure directly in aqueous solution, whereas AlphaFold
was mostly trained on protein structures in crystals. The third exists in nature as a multidomain complex
consisting of 52 identical copies of the same domain, a situation AlphaFold was not programmed to
consider. For all targets with a single domain, excluding only one very large protein and the two
structures determined by NMR, AlphaFold 2 achieved a GDT_TS score of over 80.

CASP15
In 2022, DeepMind did not enter CASP15, but most of the entrants used AlphaFold or tools incorporating
AlphaFold.[45]

Reception
AlphaFold 2 scoring more than 90 in CASP's global distance test (GDT) is considered a significant
achievement in computational biology[5] and great progress towards a decades-old grand challenge of
biology.[7] Nobel Prize winner and structural biologist Venki Ramakrishnan called the result "a stunning
advance on the protein folding problem",[5] adding that "It has occurred decades before many people in
the field would have predicted. It will be exciting to see the many ways in which it will fundamentally
change biological research."[41] Despite the enthusiasm surrounding the media and social processes AI is
not a "solution" and cannot be considered at the same level as science with explanatory power, since AI
results (https://www.technologyreview.com/2017/04/11/5113/the-dark-secret-at-the-heart-of-ai/) are
lacking this component (https://www.nature.com/news/can-we-open-the-black-box-of-ai-1.20731).

Propelled by press releases from CASP and DeepMind,[46][41] AlphaFold 2's success received wide media
attention.[47] As well as news pieces in the specialist science press, such as Nature,[7] Science,[5] MIT
Technology Review,[2] and New Scientist,[48][49] the story was widely covered by major national
newspapers,.[50][51][52][53] A frequent theme was that ability to predict protein structures accurately based
on the constituent amino acid sequence is expected to have a wide variety of benefits in the life sciences
space including accelerating advanced drug discovery and enabling better understanding of
diseases.[7][54] Some have noted that even a perfect answer to the protein prediction problem would still
leave questions about the protein folding problem—understanding in detail how the folding process
actually occurs in nature (and how sometimes they can also misfold).[55]

In 2023, Demis Hassabis and John Jumper won the Breakthrough Prize in Life Sciences[16] as well as the
Albert Lasker Award for Basic Medical Research for their management of the AlphaFold project.[56]
Hassabis and Jumper proceeded to win the Nobel Prize in Chemistry in 2024 for their work on “protein
structure prediction” with David Baker of the University of Washington.[15][57]

Source code
The open access to source code of several AlphaFold versions (excluding AlphaFold 3) has been provided
by DeepMind after requests from the scientific community.[58][59][60] Full source code of AlphaFold-3 is
expected to be provided to open access by the end of 2024.[61][62]

Database of protein models generated by AlphaFold

The AlphaFold Protein Structure Database was
AlphaFold Protein Structure Database
launched on July 22, 2021, as a joint effort between
AlphaFold and EMBL-EBI. At launch the database Content
contains AlphaFold-predicted models of protein Data types protein structure prediction
structures of nearly the full UniProt proteome of captured
humans and 20 model organisms, amounting to over
Organisms all UniProt proteomes
365,000 proteins. The database does not include
Contact
proteins with fewer than 16 or more than 2700
amino acid residues,[63] but for humans they are Research center EMBL-EBI
available in the whole batch file.[64] AlphaFold Primary citation [10]

planned to add more sequences to the collection, the Access

initial goal (as of beginning of 2022) being to cover
Website https://www.alphafold.ebi.ac.uk/
most of the UniRef90 set of more than 100 million
proteins. As of May 15, 2022, 992,316 predictions Download URL yes
were available.[65] Tools
Web yes
In July 2021, UniProt-KB and InterPro[66] has been
Miscellaneous
updated to show AlphaFold predictions when
available.[67] License CC-BY 4.0
Curation policy automatic
On July 28, 2022, the team uploaded to the database
the structures of around 200 million proteins from 1
million species, covering nearly every known protein on the planet.[68]

Limitations
AlphaFold has various limitations:

AlphaFold DB provides monomeric models of proteins, rather than their biologically relevant
complexes.[69]
Many protein regions are predicted with low confidence score, including the intrinsically
disordered protein regions.[70]
Alphafold-2 was validated for predicting structural effects of mutations with a limited
success.[71]
The model relies to some degree upon co-evolutionary information across similar proteins,
and thus may not perform well on synthetic proteins or proteins with very low homology to
anything in the database.[72]
The ability of the model to produce multiple native conformations of proteins is limited.
AlphaFold 3 version can predict structures of protein complexes with a very limited set of
selected cofactors and co- and post-translational modifications.[73] Between 50% and 70%
 of the structures of the human proteome are incomplete without covalently-attached
glycans.[74][69] AlphaFill, a derived database, adds cofactors to AlphaFold models where
appropriate.[75]
In the algorithm, the residues are moved freely, without any restraints. Therefore, during
modeling the integrity of the chain is not maintained. As a result, AlphaFold may produce
topologically wrong results, like structures with an arbitrary number of knots.[76]

Applications
AlphaFold has been used to predict structures of proteins of SARS-CoV-2, the causative agent of
COVID-19. The structures of these proteins were pending experimental detection in early 2020.[77][7]
Results were examined by the scientists at the Francis Crick Institute in the United Kingdom before
release into the larger research community. The team also confirmed accurate prediction against the
experimentally determined SARS-CoV-2 spike protein that was shared in the Protein Data Bank, an
international open-access database, before releasing the computationally determined structures of the
under-studied protein molecules.[78] The team acknowledged that although these protein structures might
not be the subject of ongoing therapeutical research efforts, they will add to the community's
understanding of the SARS-CoV-2 virus.[78] Specifically, AlphaFold 2's prediction of the structure of the
ORF3a protein was very similar to the structure determined by researchers at University of California,
Berkeley using cryo-electron microscopy. This specific protein is believed to assist the virus in breaking
out of the host cell once it replicates. This protein is also believed to play a role in triggering the
inflammatory response to the infection.[79]

Published works
Andrew W. Senior et al. (December 2019), "Protein structure prediction using multiple deep
neural networks in the 13th Critical Assessment of Protein Structure Prediction (CASP13)"
(https://onlinelibrary.wiley.com/doi/abs/10.1002/prot.25834), Proteins: Structure, Function,
Bioinformatics 87(12) 1141–1148 doi:10.1002/prot.25834 (https://doi.org/10.1002%2Fprot.2
5834)
Andrew W. Senior et al. (15 January 2020), "Improved protein structure prediction using
potentials from deep learning" (https://www.nature.com/articles/s41586-019-1923-7), Nature
577 706–710 doi:10.1038/s41586-019-1923-7 (https://doi.org/10.1038%2Fs41586-019-1923
-7)
John Jumper et al. (December 2020), "High Accuracy Protein Structure Prediction Using
Deep Learning", in Fourteenth Critical Assessment of Techniques for Protein Structure
Prediction (Abstract Book) (https://predictioncenter.org/casp14/doc/CASP14_Abstracts.pdf),
pp. 22–24
John Jumper et al. (December 2020), "AlphaFold 2 (https://predictioncenter.org/casp14/doc/
presentations/2020_12_01_TS_predictor_AlphaFold2.pdf)". Presentation given at CASP 14.

See also
Folding@home
IBM Blue Gene
Foldit
Rosetta@home
 Human Proteome Folding Project
AlphaZero
AlphaGo
AlphaGeometry
Predicted Aligned Error

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Further reading
Carlos Outeiral, CASP14: what Google DeepMind's AlphaFold 2 really achieved, and what it
 means for protein folding, biology and bioinformatics (https://www.blopig.com/blog/2020/12/c
asp14-what-google-deepminds-alphafold-2-really-achieved-and-what-it-means-for-protein-fo
lding-biology-and-bioinformatics/), Oxford Protein Informatics Group. (3 December)
Mohammed AlQuraishi, AlphaFold2 @ CASP14: "It feels like one's child has left home." (htt
ps://moalquraishi.wordpress.com/2020/12/08/alphafold2-casp14-it-feels-like-ones-child-has-
left-home/) (blog), 8 December 2020
Mohammed AlQuraishi, The AlphaFold2 Method Paper: A Fount of Good Ideas (https://moal
quraishi.wordpress.com/2021/07/25/the-alphafold2-method-paper-a-fount-of-good-ideas/)
(blog), 25 July 2021

External links
AlphaFold-3 web server (https://golgi.sandbox.google.com/about)
AlphaFold v2.1 code and links to model (https://github.com/deepmind/alphafold) on GitHub
Open access to protein structure predictions for the human proteome and 20 other key
organisms (https://alphafold.ebi.ac.uk/) at European Bioinformatics Institute (AlphaFold
Protein Structure Database)
CASP 14 (https://predictioncenter.org/casp14/index.cgi) website
AlphaFold: The making of a scientific breakthrough (https://www.youtube.com/watch?v=gg7
WjuFs8F4), DeepMind, via YouTube.
ColabFold (https://github.com/sokrypton/ColabFold) (Mirdita, Milot; Schütze, Konstantin;
Moriwaki, Yoshitaka; Heo, Lim; Ovchinnikov, Sergey; Steinegger, Martin (2022-05-30).
"ColabFold: Making protein folding accessible to all" (https://www.ncbi.nlm.nih.gov/pmc/articl
es/PMC9184281). Nature Methods. 19 (6): 679–682. doi:10.1038/s41592-022-01488-1 (http
s://doi.org/10.1038%2Fs41592-022-01488-1). PMC 9184281 (https://www.ncbi.nlm.nih.gov/
pmc/articles/PMC9184281). PMID 35637307 (https://pubmed.ncbi.nlm.nih.gov/35637307).),
version (https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold
2.ipynb) for homooligomeric prediction and complexes

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