Multiple Sequence Alignment
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Benchmarks
Most implemented
Accurate Protein Structure Prediction by Embeddings and Deep Learning Representations
ESM-NBR: fast and accurate nucleic acid-binding residue prediction via protein language model feature representation and multi-task learning
Enhancing the Protein Tertiary Structure Prediction by Multiple Sequence Alignment Generation
Phylogenetic automata, pruning, and multiple alignment
Papers
Protein Structure Prediction: From Evolutionary Constraints to Generative Modeling
Accurate protein structure prediction is fundamental to structural biology because protein structure underlies molecular function and provides a basis for mechanistic interpretation. Recent advances in deep learning have…
Protein Structure PredictionMultiple Sequence AlignmentProtein DesignBoltzmann Machine Learning with a Parallel, Persistent Markov chain Monte Carlo method for Estimating Evolutionary Fields and Couplings from a Protein Multiple Sequence Alignment
The inverse Potts problem for estimating evolutionary single-site fields and pairwise couplings in homologous protein sequences from their single-site and pairwise amino acid frequencies observed in their multiple sequen…
Multiple Sequence AlignmentTraining-Free Generation of Protein Sequences from Small Family Alignments via Stochastic Attention
Generating novel protein sequences that respect a family's statistical constraints typically requires training deep generative models on thousands to millions of examples. Yet most protein families are small: the median …
Multiple Sequence AlignmentCharacterising Behavioural Families and Dynamics of Promotional Twitter Bots via Sequence-Based Modelling
This paper asks whether promotional Twitter/X bots form behavioural families and whether members evolve similarly. We analyse 2,798,672 tweets from 2,615 ground-truth promotional bot accounts (2006-2021), focusing on com…
Multiple Sequence AlignmentClassifying Metamorphic versus Single-Fold Proteins with Statistical Learning and AlphaFold2
The remarkable success of AlphaFold2 in providing accurate atomic-level prediction of protein structures from their amino acid sequence has transformed approaches to the protein folding problem. However, its core paradig…
Protein Structure PredictionMultiple Sequence AlignmentAI-based Methods for Simulating, Sampling, and Predicting Protein Ensembles
Advances in deep learning have opened an era of abundant and accurate predicted protein structures; however, similar progress in protein ensembles has remained elusive. This review highlights several recent research dire…
Multiple Sequence Alignment