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AlphaFold 2 is here: what’s behind the structure prediction miracle
Prelude Until Thursday morning, the best answer we had was an image, published in DeepMind’s press releaseback in November. This schema made the rounds of the internet at the time, and has been featured in a multitude of conferences and discussion groups ever since. But, sadly, it was lacking in details, … See more
Feelings and other stuff I will be honest with you: all in all, after I read the paper for the first time, my feelings were very clear: I felt quite disappointed. Do not get me wrong. I think this is one of the most important scientific achievements of this century, and I do not … See more
Will DeepMind open source their AlphaFold 2 code? Yes! It is here. Is AlphaFold 2 a code that anyone can run? There won’t be an Android app anytime soon, but anyone … See more
Weirdly, I find myself having pretty much the same conclusions that I arrived at eight months ago. We know that AlphaFold 2 “works”, within some limitations, and that its release to the community will stimulate tons of novel research in biology. … See more
AlphaFold2: Reshaping Our Understanding of Protein Folding
Dec 4, 2024 · Pair Representation encodes spatial and contact relationships between residue pairs, understanding their 3D interactions. Through iterative refinements, the Evoformer …
Understanding Protein Language Models Part I: …
Jun 3, 2024 · This representation is then used to generate a measure of similarity between all possible residue pairs in the MSA representation. We then update …
- Studies of residue pair representation
Understanding Protein Language Models Part III: Structure …
Jan 22, 2025 · In the Evoformer block, row-wise (within-sequence) and column-wise (across-sequences) attention on this MSA yields information about co-evolving residues. This MSA …
Protein Residue Contacts and Prediction Methods - PMC
Residue–residue contacts (or simply “contacts”) in protein 3-D structures are pairs of spatially close residues. A 3-D structure of a protein is expressed as x, y, and z coordinates of the …
AlphaFold Architecture - uvio.bio
Dec 16, 2021 · In the Evoformer (Algorithm 6), what are the pair and MSA representations? The pair representation ($N_{res} \times N_{res} \times c$) contains sequence-specific …
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Protein–protein contact prediction by geometric triangle-aware …
Oct 19, 2023 · Here we develop a protein language model-based deep learning method to predict the inter-protein residue–residue contacts of protein complexes—named DeepInter—by …
Residue–Residue Interaction Prediction via Stacked Meta-Learning
Protein–protein interactions (PPIs) are the basis of most biological functions determined by residue–residue interactions (RRIs). Predicting residue pairs responsible for the interaction is …
Protein-Protein Interaction Interface Residue Pair Prediction
Here, we developed a novel deep network architecture called the multi-layered Long-Short Term Memory networks (LSTMs) approach for the prediction of protein interface residue pairs. First, …
Sequence representation approaches for sequence-based protein ...
Feb 2, 2021 · Here, we summarized all the main approaches that are used to represent protein sequence data (amino acid sequence encoding or embedding), which include end-to-end …
Evaluation of residue-residue contact …
May 24, 2021 · The probability (score) of a predicted residue pair given by a machine learning/deep learning/ECA model indicates the category (contact/noncontact or distance bins) to which …
AlphaFold: Protein Structure Prediction - by Alishba Imran
May 27, 2024 · The second is the outer product mean block, where the MSA representation provides a way to update the pair representation. The other transformer head that operates on …
Tetramer protein complex interface residue pairs prediction with …
Nov 1, 2020 · In this paper, we proposed a method for predicting protein-protein interface residue pairs base on deep learning, by using protein geometric and physicochemical characteristic, …
Visualizing the Residue Interaction Landscape of Proteins by …
Apr 25, 2023 · BACKGROUND: We examine the accuracy of enzyme catalytic residue predictions from a network representation of protein structure. In this model, amino acid alpha-carbons …
Protein-Protein Interaction Interface Residue Pair Prediction …
May 19, 2017 · Results: Here, we developed a novel deep network architecture called the multi-layered Long-Short Term Memory networks (LSTMs) approach for the prediction of protein …
(PDF) Protein-Protein Interaction Interface Residue Pair …
May 19, 2017 · Results: Here, we developed a novel deep network architecture called the multi-layered Long-Short Term Memory networks (LSTMs) approach for the prediction of protein …
AlphaFold 2: Attention Mechanism for Predicting 3D Protein …
Jul 29, 2022 · As mentioned before, when refining the pair representation, AF2 uses attention to process how residue pairs relate to one another in a graph representation. This graph …
Deep learning for protein secondary structure prediction: Pre and …
Jan 1, 2022 · Residue pairs and structural templates make up the pair representation. AlphaFold’s architecture consists of two main networks: Evoformer and the structure module. Evoformer …
Here we show a regression-based distance prediction method, which adopts the generative adversarial network to capture the delicate geometric relationship between residue pairs and …
How to Solve the Protein Folding Problem: AlphaFold2
Mar 11, 2023 · Free-floating body representation (blue triangles) composed of N-Cα-C; thus, each residue (r_i) has three sets of (x, y, z) coordinates χ angles of the sidechains (r , 3): represents …
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