Research graph
References from AI and machine learning in structural biology. Local targets link to admitted publications; unresolved targets remain external evidence.
Advancing structural biology through breakthroughs in AI
10.1016/j.sbi.2023.102601 · 2023 · External reference
Deep learning for computational biology
10.15252/msb.20156651 · 2016 · External reference
Accurate prediction of protein structures and interactions using a three-track neural network
10.1126/science.abj8754 · 2021 · External reference
The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution
10.1126/science.289.5481.905 · 2000 · External reference
Zhang, uniprot: the universal protein knowledgebase in 2025
2025 · External reference
Topaz-Denoise: general deep denoising models for cryoEM and cryoET
10.1038/s41467-020-18952-1 · 2020 · External reference
ilastik: interactive machine learning for (bio)image analysis
10.1038/s41592-019-0582-9 · 2019 · External reference
The protein data bank
10.1093/nar/28.1.235 · 2000 · External reference
Cryo-CARE: content-aware image restoration for cryo-transmission electron microscopy data
2019 · External reference
Structural biology: a golden era
10.1371/journal.pbio.3002187 · 2023 · External reference
a neural-network-based approach for identification of unknown proteins in X-ray crystallography and cryo-EM
10.1107/s2052252521011088 · 2022 · External reference
Automated fiducial-based alignment of cryo-electron tomography tilt series in Dynamo
2024 · External reference
Robust deep learning–based protein sequence design using ProteinMPNN
10.1126/science.add2187 · 2022 · External reference
Prop3D: A flexible, Python-based platform for machine learning with protein structural properties and biophysical data
10.1186/s12859-023-05586-5 · 2024 · External reference
Unresolved reference
2007 · External reference
Profile hidden Markov models
10.1093/bioinformatics/14.9.755 · 1998 · External reference
Features and development of Coot
10.1107/s0907444910007493 · 2010 · External reference
A neural network based predictor of residue contacts in proteins
10.1093/protein/12.1.15 · 1999 · External reference
Deciphering interaction fingerprints from protein molecular surfaces using geometric deep learning
10.1038/s41592-019-0666-6 · 2020 · External reference
The mechanisms of integral membrane protein biogenesis
10.1038/s41580-021-00413-2 · 2022 · External reference
AlphaFold-Multimer predicts cross-kingdom interactions at the plant-pathogen interface
10.1038/s41467-023-41721-9 · 2023 · External reference
DeepCentering: fully automated crystal centering using deep learning for macromolecular crystallography
10.1107/s160057751900434x · 2019 · External reference
Highly accurate protein structure prediction with AlphaFold
10.1038/s41586-021-03819-2 · 2021 · External reference
Protein secondary structure prediction based on an improved support vector machines approach
10.1093/protein/gzg072 · 2003 · External reference
The resolution revolution
10.1126/science.1251652 · 2014 · External reference
Deep learning in structural bioinformatics: current applications and future perspectives
10.1093/bib/bbae042 · 2024 · External reference
Evolutionary-scale prediction of atomic-level protein structure with a language model
10.1126/science.ade2574 · 2023 · External reference
Isotropic reconstruction for electron tomography with deep learning
2022 · External reference
Predicting locations of cryptic pockets from single protein structures using the PocketMiner graph neural network
10.1038/s41467-023-36699-3 · 2023 · External reference
UCSF ChimeraX: tools for structure building and analysis
10.1002/pro.4792 · 2023 · External reference
MMseqs2 desktop and local web server app for fast, interactive sequence searches
2019 · External reference
Deep learning improves macromolecule identification in 3D cellular cryo-electron tomograms
10.1038/s41592-021-01275-4 · 2021 · External reference
SuRVoS 2: accelerating annotation and segmentation for large volumetric bioimage workflows across modalities and scales
10.3389/fcell.2022.842342 · 2022 · External reference
DeepTracer for fast de novo cryo-EM protein structure modeling and special studies on cov-related complexes
2021 · External reference
HMMER web server: 2018 update
10.1093/nar/gky448 · 2018 · External reference
CryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination
10.1038/nmeth.4169 · 2017 · External reference
Evaluating protein transfer learning with TAPE
2019 · External reference
DeepRank-GNN: a graph neural network framework to learn patterns in protein–protein interfaces
10.1093/bioinformatics/btac759 · 2023 · External reference
CTFFIND4: fast and accurate defocus estimation from electron micrographs
10.1016/j.jsb.2015.08.008 · 2015 · External reference
RELION: implementation of a Bayesian approach to cryo-EM structure determination
10.1016/j.jsb.2012.09.006 · 2012 · External reference
Clustal omega for making accurate alignments of many protein sequences
10.1002/pro.3290 · 2018 · External reference
Pfam: multiple sequence alignments and HMM-profiles of protein domains
10.1093/nar/26.1.320 · 1998 · External reference
HH-suite3 for fast remote homology detection and deep protein annotation
10.1186/s12859-019-3019-7 · 2019 · External reference
Real-time cryo-electron microscopy data preprocessing with Warp
10.1038/s41592-019-0580-y · 2019 · External reference
10.1093/nar/gkad1199
10.1093/nar/gkad1199 · External reference
Intrinsically disordered proteins: an overview
10.3390/ijms232214050 · 2022 · External reference
Highly accurate protein structure prediction for the human proteome
10.1038/s41586-021-03828-1 · 2021 · External reference
AlphaFold protein structure database: massively expanding the structural coverage of protein-sequence space with high-accuracy models
10.1093/nar/gkab1061 · 2022 · External reference
Neural information processing systems foundation United States Attention is all you need
2017 · External reference
AI is a viable alternative to high throughput screening: a 318-target study
2024 · External reference
Molecular structure of nucleic acids: a structure for deoxyribose nucleic acid
10.1038/171737a0 · 1953 · External reference
De novo design of protein structure and function with RFdiffusion
10.1038/s41586-023-06415-8 · 2023 · External reference
A deep learning method for simultaneous denoising and missing wedge reconstruction in cryogenic electron tomography
10.1038/s41467-024-51438-y · 2024 · External reference
The way to NMR structures of proteins
10.1038/nsb1101-923 · 2001 · External reference
AlphaFold2-aware protein-DNA binding site prediction using graph transformer
10.1093/bib/bbab564 · 2022 · External reference
MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy
10.1038/nmeth.4193 · 2017 · External reference
CryoDRGN: reconstruction of heterogeneous cryo-EM structures using neural networks
10.1038/s41592-020-01049-4 · 2021 · External reference
Clustal omega for making accurate alignments of many protein sequences
10.1002/pro.3290 · ExternalCitation · doi-reference
UCSF ChimeraX: tools for structure building and analysis
10.1002/pro.4792 · ExternalCitation · doi-reference
RELION: implementation of a Bayesian approach to cryo-EM structure determination
10.1016/j.jsb.2012.09.006 · ExternalCitation · doi-reference
CTFFIND4: fast and accurate defocus estimation from electron micrographs
10.1016/j.jsb.2015.08.008 · ExternalCitation · doi-reference
Advancing structural biology through breakthroughs in AI
10.1016/j.sbi.2023.102601 · ExternalCitation · doi-reference
Molecular structure of nucleic acids: a structure for deoxyribose nucleic acid
10.1038/171737a0 · ExternalCitation · doi-reference
CryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination
10.1038/nmeth.4169 · ExternalCitation · doi-reference
MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy
10.1038/nmeth.4193 · ExternalCitation · doi-reference
The way to NMR structures of proteins
10.1038/nsb1101-923 · ExternalCitation · doi-reference
Topaz-Denoise: general deep denoising models for cryoEM and cryoET
10.1038/s41467-020-18952-1 · ExternalCitation · doi-reference
Predicting locations of cryptic pockets from single protein structures using the PocketMiner graph neural network
10.1038/s41467-023-36699-3 · ExternalCitation · doi-reference
AlphaFold-Multimer predicts cross-kingdom interactions at the plant-pathogen interface
10.1038/s41467-023-41721-9 · ExternalCitation · doi-reference
A deep learning method for simultaneous denoising and missing wedge reconstruction in cryogenic electron tomography
10.1038/s41467-024-51438-y · ExternalCitation · doi-reference
The mechanisms of integral membrane protein biogenesis
10.1038/s41580-021-00413-2 · ExternalCitation · doi-reference
Highly accurate protein structure prediction with AlphaFold
10.1038/s41586-021-03819-2 · ExternalCitation · doi-reference
Highly accurate protein structure prediction for the human proteome
10.1038/s41586-021-03828-1 · ExternalCitation · doi-reference
De novo design of protein structure and function with RFdiffusion
10.1038/s41586-023-06415-8 · ExternalCitation · doi-reference
Real-time cryo-electron microscopy data preprocessing with Warp
10.1038/s41592-019-0580-y · ExternalCitation · doi-reference
ilastik: interactive machine learning for (bio)image analysis
10.1038/s41592-019-0582-9 · ExternalCitation · doi-reference
Deciphering interaction fingerprints from protein molecular surfaces using geometric deep learning
10.1038/s41592-019-0666-6 · ExternalCitation · doi-reference
CryoDRGN: reconstruction of heterogeneous cryo-EM structures using neural networks
10.1038/s41592-020-01049-4 · ExternalCitation · doi-reference
Deep learning improves macromolecule identification in 3D cellular cryo-electron tomograms
10.1038/s41592-021-01275-4 · ExternalCitation · doi-reference
AlphaFold2-aware protein-DNA binding site prediction using graph transformer
10.1093/bib/bbab564 · ExternalCitation · doi-reference
Deep learning in structural bioinformatics: current applications and future perspectives
10.1093/bib/bbae042 · ExternalCitation · doi-reference
Profile hidden Markov models
10.1093/bioinformatics/14.9.755 · ExternalCitation · doi-reference
DeepRank-GNN: a graph neural network framework to learn patterns in protein–protein interfaces
10.1093/bioinformatics/btac759 · ExternalCitation · doi-reference
Pfam: multiple sequence alignments and HMM-profiles of protein domains
10.1093/nar/26.1.320 · ExternalCitation · doi-reference
The protein data bank
10.1093/nar/28.1.235 · ExternalCitation · doi-reference
AlphaFold protein structure database: massively expanding the structural coverage of protein-sequence space with high-accuracy models
10.1093/nar/gkab1061 · ExternalCitation · doi-reference
10.1093/nar/gkad1199
10.1093/nar/gkad1199 · ExternalCitation · doi-reference
HMMER web server: 2018 update
10.1093/nar/gky448 · ExternalCitation · doi-reference
A neural network based predictor of residue contacts in proteins
10.1093/protein/12.1.15 · ExternalCitation · doi-reference
Protein secondary structure prediction based on an improved support vector machines approach
10.1093/protein/gzg072 · ExternalCitation · doi-reference
Features and development of Coot
10.1107/s0907444910007493 · ExternalCitation · doi-reference
DeepCentering: fully automated crystal centering using deep learning for macromolecular crystallography
10.1107/s160057751900434x · ExternalCitation · doi-reference
a neural-network-based approach for identification of unknown proteins in X-ray crystallography and cryo-EM
10.1107/s2052252521011088 · ExternalCitation · doi-reference
The resolution revolution
10.1126/science.1251652 · ExternalCitation · doi-reference
The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution
10.1126/science.289.5481.905 · ExternalCitation · doi-reference
Accurate prediction of protein structures and interactions using a three-track neural network
10.1126/science.abj8754 · ExternalCitation · doi-reference
Robust deep learning–based protein sequence design using ProteinMPNN
10.1126/science.add2187 · ExternalCitation · doi-reference
Evolutionary-scale prediction of atomic-level protein structure with a language model
10.1126/science.ade2574 · ExternalCitation · doi-reference
HH-suite3 for fast remote homology detection and deep protein annotation
10.1186/s12859-019-3019-7 · ExternalCitation · doi-reference
Prop3D: A flexible, Python-based platform for machine learning with protein structural properties and biophysical data
10.1186/s12859-023-05586-5 · ExternalCitation · doi-reference
Structural biology: a golden era
10.1371/journal.pbio.3002187 · ExternalCitation · doi-reference
Deep learning for computational biology
10.15252/msb.20156651 · ExternalCitation · doi-reference
SuRVoS 2: accelerating annotation and segmentation for large volumetric bioimage workflows across modalities and scales
10.3389/fcell.2022.842342 · ExternalCitation · doi-reference
Intrinsically disordered proteins: an overview
10.3390/ijms232214050 · ExternalCitation · doi-reference
