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- Residue pairs are represented by 3 descriptors that are transformation invariant: backbone distance d b , sidechain distance d s , and angle θ. This constitutes a compact representation of residue pairs and enables quick retrieval of similar pairs. https://doi.org/10.1371/journal.pcbi.1008502.g004
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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 …
The pair representation is intended to represent a set of distances between residues of the protein, but distances in Euclidean space respect the triangle inequality, so we need to enforce …
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 information …
Pair Representation: The pair representation is initialized as the positional embedding, based on the residue index, of the protein. The process involves computing the relative distances by …
Oct 18, 2023 · Here, we leverage the internal pairwise representation of AlphaFold2 (AF2) to train a model, AF2BIND, to accurately predict small-molecule-binding residues given only a target …
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 …
Evaluation of residue-residue contact prediction …
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 the residue pair is most similar. …
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 …
Protein structure prediction with in-cell photo-crosslinking mass ...
Mar 20, 2023 · To test AlphaLink, we perform a large-scale crosslinking MS study with photo-L, identifying 615 in situ residue–residue contacts in Escherichia coli membrane fractions, …
Understanding Protein Language Models: Multiple Sequence …
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 the pair representation of …
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 …
Highly accurate protein structure prediction with AlphaFold
Jul 15, 2021 · First, the final pair representation is linearly projected to a binned distance distribution (distogram) prediction, scored with a cross-entropy loss.
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 …
How does DeepMind AlphaFold2 work? - Boris Burkov
Dec 25, 2021 · If 3D structure template was available, AF2 constructs a pair representation of distances between residues in the protein from that template. If it was not available, it …
Representation of residue pairs. Residue pairs are represented …
Residue pairs are represented by 3 descriptors that are transformation invariant: backbone distance d b , sidechain distance d s , and angle θ. This constitutes a compact representation of...
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, …
Use of residue pairs in protein sequence-sequence and …
Each element of H2 or T2 measures the frequency with which a pair of amino acid types in one protein, k-residues apart in the sequence, is aligned with another pair of residues, of given …
Residue–Residue Interaction Prediction via Stacked Meta …
Apr 30, 2021 · Protein–protein interactions (PPIs) are the basis of most biological functions determined by residue–residue interactions (RRIs). Predicting residue pairs responsible for the …
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 …
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