ArticleScientific reports2021
Analyzing effect of quadruple multiple sequence alignments on deep learning based protein inter-residue distance prediction.
Article in Scientific reports, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Computational approaches for RNA structure prediction and design.Cell reports. Physical science · 2026Article
- Structure Modeling Protocols for Protein Multimer and RNA in CASP16 With Enhanced MSAs, Model Ranking, and Deep Learning.Proteins · 2026Article
- Distance-AF improves predicted protein structure models by AlphaFold2 with user-specified distance constraints.Communications biology · 2025Article
- BloodProST: prediction of blood-secretory proteins through self-training.Briefings in bioinformatics · 2025Article
- GO2Sum: generating human-readable functional summary of proteins from GO terms.NPJ systems biology and applications · 2024Article
- Free-Docking and Template-Based Docking: Physics Versus Knowledge-Based Docking.Methods in molecular biology (Clifton, N.J.) · 2024Article
- A Machine Learning Method to Identify Umami Peptide Sequences by Using Multiplicative LSTM Embedded Features.Foods (Basel, Switzerland) · 2023Article
- Pairwise and Multi-chain Protein Docking Enhanced Using LZerD Web Server.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Protein Structural Modeling for Electron Microscopy Maps Using VESPER and MAINMAST.Current protocols · 2022Article
- ContactPFP: Protein function prediction using predicted contact information.Frontiers in bioinformatics · 2022Article
- Real-time structure search and structure classification for AlphaFold protein models.Communications biology · 2022Article
- Inter-Residue Distance Prediction From Duet Deep Learning Models.Frontiers in genetics · 2022Article
- RL-MLZerD: Multimeric protein docking using reinforcement learning.Frontiers in molecular biosciences · 2022Article
- Article
- DeepSec: a deep learning framework for secreted protein discovery in human body fluids.Bioinformatics (Oxford, England) · 2021Article
- Article
- Evaluation of Deep Neural Network ProSPr for Accurate Protein Distance Predictions on CASP14 Targets.International journal of molecular sciences · 2021Article
- Deep Learning-Based Advances in Protein Structure Prediction.International journal of molecular sciences · 2021Review
- LZerD Protein-Protein Docking Webserver Enhanced WithFrontiers in molecular biosciences · 2021Review
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Authors and funding
6 authors.
Funding
Abstract
Protein 3D structure prediction has advanced significantly in recent years due to improving contact prediction accuracy. This improvement has been largely due to deep learning approaches that predict inter-residue contacts and, more recently, distances using multiple sequence alignments (MSAs). In this work we present AttentiveDist, a novel approach that uses different MSAs generated with different E-values in a single model to increase the co-evolutionary information provided to the model. To determine the importance of each MSA's feature at the inter-residue level, we added an attention layer to the deep neural network. We show that combining four MSAs of different E-value cutoffs improved the model prediction performance as compared to single E-value MSA features. A further improvement was observed when an attention layer was used and even more when additional prediction tasks of bond angle predictions were added. The improvement of distance predictions were successfully transferred to achieve better protein tertiary structure modeling.
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