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Improved protein structure prediction with trRosettaX2 , AlphaFold2 , and optimized MSAs in CASP15

https://doi.org/10.1002/prot.26570
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/advs.202102592openalex-snapshot
Improved Protein Structure Prediction Using a New Multi‐Scale Network and Homologous Templates
inferredcites →https://doi.org/10.1002/prot.20264openalex-snapshot
Scoring function for automated assessment of protein structure template quality
inferredcites →https://doi.org/10.1002/prot.26197openalex-snapshot
Protein oligomer modeling guided by predicted interchain contacts in CASP14
inferredcites →https://doi.org/10.1016/j.sbi.2022.102495openalex-snapshot
Protein structure prediction in the deep learning era
inferredcites →https://doi.org/10.1016/s0076-6879(04)83004-0openalex-snapshot
Protein Structure Prediction Using Rosetta
inferredcites →https://doi.org/10.1038/d41586-022-04438-1openalex-snapshot
After AlphaFold: protein-folding contest seeks next big breakthrough
inferredcites →https://doi.org/10.1038/nbt.3988openalex-snapshot
MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets
inferredcites →https://doi.org/10.1038/nmeth.1818openalex-snapshot
HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment
inferredcites →https://doi.org/10.1038/s41467-022-29394-2openalex-snapshot
AF2Complex predicts direct physical interactions in multimeric proteins with deep learning
inferredcites →https://doi.org/10.1038/s41586-021-03819-2openalex-snapshot
Highly accurate protein structure prediction with AlphaFold
inferredcites →https://doi.org/10.1073/pnas.1914677117openalex-snapshot
Improved protein structure prediction using predicted interresidue orientations
inferredcites →https://doi.org/10.1093/bioinformatics/btab632openalex-snapshot
Improved estimation of model quality using predicted inter-residue distance
inferredcites →https://doi.org/10.1093/bioinformatics/btab781openalex-snapshot
Toward the assessment of predicted inter-residue distance
inferredcites →https://doi.org/10.1093/bioinformatics/btac056openalex-snapshot
DeepUMQA: ultrafast shape recognition-based protein model quality assessment using deep learning
inferredcites →https://doi.org/10.1093/bioinformatics/btad070openalex-snapshot
A unified approach to protein domain parsing with inter-residue distance matrix
inferredcites →https://doi.org/10.1093/bioinformatics/btu744openalex-snapshot
DISOPRED3: precise disordered region predictions with annotated protein-binding activity
inferredcites →https://doi.org/10.1093/bioinformatics/btz477openalex-snapshot
Protein contact prediction using metagenome sequence data and residual neural networks
inferredcites →https://doi.org/10.1093/nar/gkt263openalex-snapshot
Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions
inferredcites →https://doi.org/10.1093/nar/gkv342openalex-snapshot
I-TASSER server: new development for protein structure and function predictions
inferredcites →https://doi.org/10.1093/nar/gkw1081openalex-snapshot
Uniclust databases of clustered and deeply annotated protein sequences and alignments
inferredcites →https://doi.org/10.1101/2021.10.04.463034openalex-snapshot
Protein complex prediction with AlphaFold-Multimer
inferredcites →https://doi.org/10.1126/science.abj8754openalex-snapshot
Accurate prediction of protein structures and interactions using a three-track neural network
inferredcites →https://doi.org/10.1371/journal.pone.0161879openalex-snapshot
DockQ: A Quality Measure for Protein-Protein Docking Models

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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An Easy-to-Use Three-Dimensional Protein Structure Prediction Platform Based on Deep Learning
inferred← citeshttps://doi.org/10.1002/advs.202518469openalex-snapshot
Generating Dynamic Structures Through Physics‐Based Sampling of Predicted Inter‐Residue Geometries
inferred← citeshttps://doi.org/10.1002/prot.26593openalex-snapshot
Tertiary structure assessment at CASP15
inferred← citeshttps://doi.org/10.1002/prot.26617openalex-snapshot
Critical assessment of methods of protein structure prediction ( CASP )—Round XV
inferred← citeshttps://doi.org/10.1002/prot.70016openalex-snapshot
Docking With Rosetta and Deep Learning Approaches in CAPRI Rounds 47–55
inferred← citeshttps://doi.org/10.1002/prot.70017openalex-snapshot
Predicting the Oligomeric State of Proteins Using Multiple Templates Detected by Complementary Alignment Methods
inferred← citeshttps://doi.org/10.1002/prot.70030openalex-snapshot
Accurate Biomolecular Structure Prediction in CASP16 With Optimized Inputs to State‐Of‐The‐Art Predictors
inferred← citeshttps://doi.org/10.1002/prot.70031openalex-snapshot
CASP16 Protein Monomer Structure Prediction Assessment
inferred← citeshttps://doi.org/10.1002/prot.70033openalex-snapshot
Structure Modeling Protocols for Protein Multimer and RNA in CASP16 With Enhanced MSAs , Model Ranking, and Deep Learning
inferred← citeshttps://doi.org/10.1016/j.compbiolchem.2026.109076openalex-snapshot
DeepStruct: Multi-modal deep learning integrating omics and energy scoring for protein structure prediction in plants
inferred← citeshttps://doi.org/10.1016/j.compbiomed.2025.110033openalex-snapshot
The proteomic code: Novel amino acid residue pairing models “encode” protein folding and protein-protein interactions
inferred← citeshttps://doi.org/10.1016/j.copbio.2023.103047openalex-snapshot
Valorization of single-carbon chemicals by using carboligases as key enzymes
inferred← citeshttps://doi.org/10.1016/j.crstbi.2024.100163openalex-snapshot
An easy-to-use three-dimensional protein-structure-prediction online platform "DPL3D" based on deep learning algorithms
inferred← citeshttps://doi.org/10.1016/j.csbj.2025.01.017openalex-snapshot
Physical-aware model accuracy estimation for protein complex using deep learning method
inferred← citeshttps://doi.org/10.1016/j.sbi.2025.102985openalex-snapshot
Advancing protein structure prediction beyond AlphaFold2
inferred← citeshttps://doi.org/10.1016/j.sbi.2026.103247openalex-snapshot
Artificial intelligence methods for protein structure and interaction prediction: Recent advances and challenges
inferred← citeshttps://doi.org/10.1021/acs.jcim.3c01324openalex-snapshot
Recent Advances and Challenges in Protein Structure Prediction
inferred← citeshttps://doi.org/10.1021/acs.jcim.6c00829openalex-snapshot
TriGraphQA: A Triple Graph Learning Framework for Model Quality Assessment of Protein Complexes
inferred← citeshttps://doi.org/10.1038/s41467-025-65090-7openalex-snapshot
High-accuracy protein complex structure modeling based on sequence-derived structure complementarity
inferred← citeshttps://doi.org/10.1038/s41596-024-01060-5openalex-snapshot
Easy and accurate protein structure prediction using ColabFold
inferred← citeshttps://doi.org/10.1038/s42256-024-00873-zopenalex-snapshot
Integrated structure prediction of protein–protein docking with experimental restraints using ColabDock
inferred← citeshttps://doi.org/10.1039/d5ra05395aopenalex-snapshot
Are we there yet with XNA aptamers?
inferred← citeshttps://doi.org/10.1089/phage.2023.0041openalex-snapshot
The TolC and Lipopolysaccharide-Specific Escherichia coli Bacteriophage TLS—the Tlsvirus Archetype Virus
inferred← citeshttps://doi.org/10.1093/bib/bbaf616openalex-snapshot
A comprehensive benchmarking of the AlphaFold3 for predicting biomacromolecules and their interactions
inferred← citeshttps://doi.org/10.1093/bioinformatics/btad712openalex-snapshot
DeepFold: enhancing protein structure prediction through optimized loss functions, improved template features, and re-optimized energy function
inferred← citeshttps://doi.org/10.1093/bioinformatics/btaf432openalex-snapshot
AF3Complex yields improved structural predictions of protein complexes
inferred← citeshttps://doi.org/10.1101/2023.09.05.556364openalex-snapshot
Rosetta Energy Analysis of AlphaFold2 models: Point Mutations and Conformational Ensembles
inferred← citeshttps://doi.org/10.1109/iiswc66894.2025.00046openalex-snapshot
AlphaFold3 Workload Characterization: A Comprehensive Analysis of Bottlenecks and Performance Scaling
inferred← citeshttps://doi.org/10.11648/j.innov.20250603.20openalex-snapshot
The Role of Artificial Intelligence in Protein Structural and Functional Prediction: Current Status and Future Prospective
inferred← citeshttps://doi.org/10.22541/au.169658651.11658182/v1openalex-snapshot
Critical Assessment of Methods of Protein Structure Prediction (CASP) – Round XV
inferred← citeshttps://doi.org/10.3390/biom14121531openalex-snapshot
The Historical Evolution and Significance of Multiple Sequence Alignment in Molecular Structure and Function Prediction
inferred← citeshttps://doi.org/10.64898/2026.04.14.718427openalex-snapshot
Benchmarking MSA pairing for protein-protein complex structure prediction reveals a depth-over-pairing principle
inferred← citeshttps://doi.org/10.64898/2026.06.05.730531openalex-snapshot
DDI_single: Single-Sequence-Based Protein Domain Assembly
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