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AlphaFold at CASP13

https://doi.org/10.1093/bioinformatics/btz422

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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/(sici)1097-0134(1999)37:3+<22::aid-prot5>3.0.co;2-wopenalex-snapshot

Processing and analysis of CASP3 protein structure predictions

inferredcites →https://doi.org/10.1002/prot.21662openalex-snapshot

Assessment of CASP7 predictions in the high accuracy template-based modeling category

inferredcites →https://doi.org/10.1002/prot.24974openalex-snapshot

Improved de novo structure prediction in CASP 11 by incorporating coevolution information into Rosetta

inferredcites →https://doi.org/10.1002/prot.25064openalex-snapshot

Critical assessment of methods of protein structure prediction: Progress and new directions in round XI

inferredcites →https://doi.org/10.1002/prot.25407openalex-snapshot

Assessment of contact predictions in CASP12: Co‐evolution and deep learning coming of age

inferredcites →https://doi.org/10.1002/prot.25414openalex-snapshot

Template‐based and free modeling of I‐TASSER and QUARK pipelines using predicted contact maps in CASP12

inferredcites →https://doi.org/10.1002/prot.25415openalex-snapshot

Critical assessment of methods of protein structure prediction (CASP)—Round XII

inferredcites →https://doi.org/10.1006/jmbi.1996.0175openalex-snapshot

Statistical Potentials Extracted From Protein Structures: How Accurate Are They?

inferredcites →https://doi.org/10.1016/b978-0-12-381270-4.00019-6openalex-snapshot

Rosetta3

inferredcites →https://doi.org/10.1016/j.cels.2017.11.014openalex-snapshot

Enhancing Evolutionary Couplings with Deep Convolutional Neural Networks

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End-to-End Differentiable Learning of Protein Structure

inferredcites →https://doi.org/10.1016/j.str.2012.04.003openalex-snapshot

A Position-Specific Distance-Dependent Statistical Potential for Protein Structure and Functional Study

inferredcites →https://doi.org/10.1016/s0022-2836(05)80269-4openalex-snapshot

Calculation of conformational ensembles from potentials of mena force

inferredcites →https://doi.org/10.1016/s0076-6879(04)83004-0openalex-snapshot

Protein Structure Prediction Using Rosetta

inferredcites →https://doi.org/10.1016/s0898-1221(96)90463-0openalex-snapshot

Advances in neural information processing systems 7

inferredcites →https://doi.org/10.1021/jm049314dopenalex-snapshot

A Knowledge-Based Energy Function for Protein−Ligand, Protein−Protein, and Protein−DNA Complexes

inferredcites →https://doi.org/10.1038/nature14539openalex-snapshot

Deep learning

inferredcites →https://doi.org/10.1038/nmeth.3213openalex-snapshot

The I-TASSER Suite: protein structure and function prediction

inferredcites →https://doi.org/10.1038/s41592-019-0598-1openalex-snapshot

Unified rational protein engineering with sequence-based deep representation learning

inferredcites →https://doi.org/10.1073/pnas.0805923106openalex-snapshot

Identification of direct residue contacts in protein–protein interaction by message passing

inferredcites →https://doi.org/10.1073/pnas.1314045110openalex-snapshot

Assessing the utility of coevolution-based residue–residue contact predictions in a sequence- and structure-rich era

inferredcites →https://doi.org/10.1073/pnas.1821309116openalex-snapshot

Distance-based protein folding powered by deep learning

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Updating Quasi-Newton Matrices with Limited Storage

inferredcites →https://doi.org/10.1093/bioinformatics/btr638openalex-snapshot

PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments

inferredcites →https://doi.org/10.1093/bioinformatics/bty178openalex-snapshot

Learned protein embeddings for machine learning

inferredcites →https://doi.org/10.1093/bioinformatics/bty278openalex-snapshot

Protein threading using residue co-variation and deep learning

inferredcites →https://doi.org/10.1107/s0907444998003254openalex-snapshot

Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination

inferredcites →https://doi.org/10.1214/lnms/1215455556openalex-snapshot

Correlated mutations in models of protein sequences: phylogenetic and structural effects

inferredcites →https://doi.org/10.12688/f1000research.11543.1openalex-snapshot

Co-evolution techniques are reshaping the way we do structural bioinformatics

inferredcites →https://doi.org/10.1371/journal.pcbi.1005324openalex-snapshot

Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model

inferredcites →https://doi.org/10.1371/journal.pone.0028766openalex-snapshot

Protein 3D Structure Computed from Evolutionary Sequence Variation

inferredcites →https://doi.org/10.1515/bams-2014-0013openalex-snapshot

Opportunities and limitations in applying coevolution-derived contacts to protein structure prediction

inferredcites →https://doi.org/10.2139/ssrn.3239970openalex-snapshot

End-to-End Differentiable Learning of Protein Structure

inferredcites →https://doi.org/10.7551/mitpress/7503.001.0001openalex-snapshot

Advances in Neural Information Processing Systems 19

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inferred← citeshttps://doi.org/10.1007/978-981-19-7911-8_6openalex-snapshot

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inferred← citeshttps://doi.org/10.1007/978-981-97-1432-2_5openalex-snapshot

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inferred← citeshttps://doi.org/10.1007/978-981-99-9621-6_22openalex-snapshot

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inferred← citeshttps://doi.org/10.1007/s00018-023-04765-0openalex-snapshot

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inferred← citeshttps://doi.org/10.1007/s00894-025-06392-xopenalex-snapshot

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inferred← citeshttps://doi.org/10.1007/s10817-024-09704-7openalex-snapshot

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inferred← citeshttps://doi.org/10.1016/b978-0-12-823021-3.00010-5openalex-snapshot

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inferred← citeshttps://doi.org/10.1016/b978-0-323-95502-7.00114-7openalex-snapshot

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Protocol for Protein Structure Modeling

inferred← citeshttps://doi.org/10.1016/bs.mcb.2022.02.001openalex-snapshot

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inferred← citeshttps://doi.org/10.1016/j.ailsci.2025.100136openalex-snapshot

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inferred← citeshttps://doi.org/10.1016/j.bbapap.2025.141100openalex-snapshot

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inferred← citeshttps://doi.org/10.1016/j.biochi.2022.11.009openalex-snapshot

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inferred← citeshttps://doi.org/10.1016/j.bioorg.2023.106894openalex-snapshot

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inferred← citeshttps://doi.org/10.1016/j.biotechadv.2026.108977openalex-snapshot

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inferred← citeshttps://doi.org/10.1016/j.bmcl.2021.127852openalex-snapshot

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inferred← citeshttps://doi.org/10.1016/j.bpj.2024.01.026openalex-snapshot

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inferred← citeshttps://doi.org/10.1016/j.bpj.2024.04.001openalex-snapshot

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inferred← citeshttps://doi.org/10.1016/j.cbpa.2021.04.005openalex-snapshot

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inferred← citeshttps://doi.org/10.1016/j.ccr.2022.214593openalex-snapshot

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inferred← citeshttps://doi.org/10.1016/j.compbiomed.2022.105695openalex-snapshot

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inferred← citeshttps://doi.org/10.1016/j.compbiomed.2024.108620openalex-snapshot

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inferred← citeshttps://doi.org/10.1016/j.csbj.2020.11.007openalex-snapshot

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inferred← citeshttps://doi.org/10.1016/j.csbj.2020.11.052openalex-snapshot

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inferred← citeshttps://doi.org/10.1016/j.csbj.2021.03.004openalex-snapshot

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inferred← citeshttps://doi.org/10.1016/j.csbj.2021.11.021openalex-snapshot

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inferred← citeshttps://doi.org/10.1016/j.fmre.2022.01.037openalex-snapshot

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inferred← citeshttps://doi.org/10.1016/j.fmre.2024.02.011openalex-snapshot

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inferred← citeshttps://doi.org/10.1016/j.ijpara.2021.10.003openalex-snapshot

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inferred← citeshttps://doi.org/10.1016/j.ipha.2025.04.001openalex-snapshot

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inferred← citeshttps://doi.org/10.1016/j.jbc.2023.104579openalex-snapshot

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inferred← citeshttps://doi.org/10.1016/j.jcp.2022.110939openalex-snapshot

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inferred← citeshttps://doi.org/10.1016/j.jinorgbio.2022.112025openalex-snapshot

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inferred← citeshttps://doi.org/10.1016/j.jmb.2021.167160openalex-snapshot

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inferred← citeshttps://doi.org/10.1016/j.jsb.2022.107920openalex-snapshot

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inferred← citeshttps://doi.org/10.1016/j.molimm.2021.07.020openalex-snapshot

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inferred← citeshttps://doi.org/10.1016/j.patter.2020.100142openalex-snapshot

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inferred← citeshttps://doi.org/10.1016/j.pestbp.2025.106816openalex-snapshot

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inferred← citeshttps://doi.org/10.1016/j.sbi.2020.07.003openalex-snapshot

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inferred← citeshttps://doi.org/10.1016/j.sbi.2024.102819openalex-snapshot

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inferred← citeshttps://doi.org/10.1016/j.sbi.2025.103218openalex-snapshot

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inferred← citeshttps://doi.org/10.1016/j.str.2021.06.008openalex-snapshot

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inferred← citeshttps://doi.org/10.1016/j.taml.2025.100629openalex-snapshot

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inferred← citeshttps://doi.org/10.1016/j.teac.2025.e00290openalex-snapshot

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inferred← citeshttps://doi.org/10.1016/j.tips.2021.04.001openalex-snapshot

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inferred← citeshttps://doi.org/10.1016/j.vaccine.2025.128051openalex-snapshot

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inferred← citeshttps://doi.org/10.1016/j.xinn.2021.100179openalex-snapshot

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inferred← citeshttps://doi.org/10.1016/j.ymben.2020.10.005openalex-snapshot

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inferred← citeshttps://doi.org/10.1021/acs.chemrev.1c00222openalex-snapshot

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inferred← citeshttps://doi.org/10.1021/acs.jcim.0c01160openalex-snapshot

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inferred← citeshttps://doi.org/10.1021/acs.jcim.3c01324openalex-snapshot

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inferred← citeshttps://doi.org/10.1021/acs.jcim.4c01475openalex-snapshot

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inferred← citeshttps://doi.org/10.1021/acssynbio.0c00454openalex-snapshot

Rational Design of a Split Flavin-Based Fluorescent Reporter

inferred← citeshttps://doi.org/10.1038/s41372-023-01719-zopenalex-snapshot

Artificial intelligence in the neonatal intensive care unit: the time is now

inferred← citeshttps://doi.org/10.1038/s41467-022-29268-7openalex-snapshot

Current progress and open challenges for applying deep learning across the biosciences

inferred← citeshttps://doi.org/10.1038/s41467-026-69084-xopenalex-snapshot

Neuromorphic photonic computing with an electro-optic analog memory

inferred← citeshttps://doi.org/10.1038/s41564-022-01204-xopenalex-snapshot

Mycobacterium abscessus pathogenesis identified by phenogenomic analyses

inferred← citeshttps://doi.org/10.1038/s41580-019-0176-5openalex-snapshot

Setting the standards for machine learning in biology

inferred← citeshttps://doi.org/10.1038/s41586-024-07146-0openalex-snapshot

Artificial intelligence and illusions of understanding in scientific research

inferred← citeshttps://doi.org/10.1038/s41592-023-01940-wopenalex-snapshot

CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning

inferred← citeshttps://doi.org/10.1038/s41594-021-00650-1openalex-snapshot

AlphaFold2 and the future of structural biology

inferred← citeshttps://doi.org/10.1038/s41598-020-61205-wopenalex-snapshot

Neighborhood Preference of Amino Acids in Protein Structures and its Applications in Protein Structure Assessment

inferred← citeshttps://doi.org/10.1038/s41598-021-91827-7openalex-snapshot

DNCON2_Inter: predicting interchain contacts for homodimeric and homomultimeric protein complexes using multiple sequence alignments of monomers and deep learning

inferred← citeshttps://doi.org/10.1038/s41598-022-20390-6openalex-snapshot

Confrontation of AlphaFold models with experimental structures enlightens conformational dynamics supporting CYP102A1 functions

inferred← citeshttps://doi.org/10.1038/s41598-025-17022-0openalex-snapshot

A comprehensive application of FiveFold for conformation ensemble-based protein structure prediction

inferred← citeshttps://doi.org/10.1038/s42003-022-03411-yopenalex-snapshot

Validated determination of NRG1 Ig-like domain structure by mass spectrometry coupled with computational modeling

inferred← citeshttps://doi.org/10.1038/s42003-022-03552-0openalex-snapshot

Inframe insertion and splice site variants in MFGE8 associate with protection against coronary atherosclerosis

inferred← citeshttps://doi.org/10.1038/s42003-024-06161-1openalex-snapshot

Optimized model architectures for deep learning on genomic data

inferred← citeshttps://doi.org/10.1038/s42003-025-09458-xopenalex-snapshot

Nanobodies as tools for studying human frataxin biology

inferred← citeshttps://doi.org/10.1038/s42256-019-0086-4openalex-snapshot

Protein structure prediction beyond AlphaFold

inferred← citeshttps://doi.org/10.1038/s42256-020-00266-yopenalex-snapshot

Understanding adversarial examples requires a theory of artefacts for deep learning

inferred← citeshttps://doi.org/10.1038/s44431-026-00025-wopenalex-snapshot

Advancements in characterization of protein dynamics with machine learning

inferred← citeshttps://doi.org/10.1039/9781839166433-00315openalex-snapshot

Reconstructing Glycosylation: How to Rebuild Glycoproteins by Molecular Dynamics-generated 3D Libraries

inferred← citeshttps://doi.org/10.1039/c9cp06554gopenalex-snapshot

A review of mathematical representations of biomolecular data

inferred← citeshttps://doi.org/10.1039/d1np00014dopenalex-snapshot

Metabolomics and complementary techniques to investigate the plant phytochemical cosmos

inferred← citeshttps://doi.org/10.1039/d4cs00196fopenalex-snapshot

Navigating the landscape of enzyme design: from molecular simulations to machine learning

inferred← citeshttps://doi.org/10.1055/s-0040-1701983openalex-snapshot

From Patient Engagement to Precision Oncology: Leveraging Informatics to Advance Cancer Care

inferred← citeshttps://doi.org/10.1063/5.0146296openalex-snapshot

Machine learning for shock compression of solids using scarce data

inferred← citeshttps://doi.org/10.1080/07391102.2024.2302937openalex-snapshot

MehNet: a vigesimal-based model by amino acid melting points generates unique ID numbers for protein sequences

inferred← citeshttps://doi.org/10.1080/07391102.2024.2445767openalex-snapshot

Investigation of bioremediation for glyphosate and its metabolite in soil using arbuscular mycorrhizal GmHsp60 protein: a molecular docking and molecular dynamics simulations approach

inferred← citeshttps://doi.org/10.1086/714960openalex-snapshot

Black Boxes or Unflattering Mirrors? Comparative Bias in the Science of Machine Behaviour

inferred← citeshttps://doi.org/10.1088/1742-6596/2533/1/012006openalex-snapshot

Casting Rubik’s Group into a Unitary Representation for Reinforcement Learning

inferred← citeshttps://doi.org/10.1088/1751-8121/ac2596openalex-snapshot

Solving Rubik’s cube via quantum mechanics and deep reinforcement learning

inferred← citeshttps://doi.org/10.1088/1757-899x/1140/1/012018openalex-snapshot

Assistance Method for the Application-Driven Design of Machine Learning Algorithms

inferred← citeshttps://doi.org/10.1093/bib/bbaa144openalex-snapshot

FoldRec-C2C: protein fold recognition by combining cluster-to-cluster model and protein similarity network

inferred← citeshttps://doi.org/10.1093/bib/bbaa362openalex-snapshot

The impact of structural bioinformatics tools and resources on SARS-CoV-2 research and therapeutic strategies

inferred← citeshttps://doi.org/10.1093/bib/bbab296openalex-snapshot

Distance-guided protein folding based on generalized descent direction

inferred← citeshttps://doi.org/10.1093/bib/bbab463openalex-snapshot

Multi contact-based folding method forde novoprotein structure prediction

inferred← citeshttps://doi.org/10.1093/bib/bbac025openalex-snapshot

Systematic evaluation of computational tools to predict the effects of mutations on protein stability in the absence of experimental structures

inferred← citeshttps://doi.org/10.1093/bib/bbac499openalex-snapshot

DeepHomo2.0: improved protein–protein contact prediction of homodimers by transformer-enhanced deep learning

inferred← citeshttps://doi.org/10.1093/bib/bbad065openalex-snapshot

A review of enzyme design in catalytic stability by artificial intelligence

inferred← citeshttps://doi.org/10.1093/bib/bbae539openalex-snapshot

DeepCheck: multitask learning aids in assessing microbial genome quality

inferred← citeshttps://doi.org/10.1093/bioinformatics/btaa003openalex-snapshot

UDSMProt: universal deep sequence models for protein classification

inferred← citeshttps://doi.org/10.1093/bioinformatics/btaa193openalex-snapshot

CRiSP: accurate structure prediction of disulfide-rich peptides with cystine-specific sequence alignment and machine learning

inferred← citeshttps://doi.org/10.1093/bioinformatics/btab484openalex-snapshot

MMpred: a distance-assisted multimodal conformation sampling for de novo protein structure prediction

inferred← citeshttps://doi.org/10.1093/bioinformatics/btab500openalex-snapshot

A sequential niche multimodal conformational sampling algorithm for protein structure prediction

inferred← citeshttps://doi.org/10.1093/bioinformatics/btab620openalex-snapshot

A de novo protein structure prediction by iterative partition sampling, topology adjustment and residue-level distance deviation optimization

inferred← citeshttps://doi.org/10.1093/bioinformatics/btab666openalex-snapshot

ProFitFun: a protein tertiary structure fitness function for quantifying the accuracies of model structures

inferred← citeshttps://doi.org/10.1093/bioinformatics/btac056openalex-snapshot

DeepUMQA: ultrafast shape recognition-based protein model quality assessment using deep learning

inferred← citeshttps://doi.org/10.1093/bioinformatics/btaf515openalex-snapshot

Graph neural network and diffusion model for modeling RNA interatomic interactions

inferred← citeshttps://doi.org/10.1093/nar/gkac1253openalex-snapshot

HybridRNAbind: prediction of RNA interacting residues across structure-annotated and disorder-annotated proteins

inferred← citeshttps://doi.org/10.1093/nar/gkad726openalex-snapshot

When will RNA get its AlphaFold moment?

inferred← citeshttps://doi.org/10.1093/plcell/koaf109openalex-snapshot

The resistance awakens: Diversity at the DNA, RNA, and protein levels informs engineering of plant immune receptors from Arabidopsis to crops

inferred← citeshttps://doi.org/10.1093/toxsci/kfad113openalex-snapshot

Mechanistic toxicology in light of genetic compensation

inferred← citeshttps://doi.org/10.1094/mpmi-03-21-0071-ropenalex-snapshot

Computational Structural Genomics Unravels Common Folds and Novel Families in the Secretome of Fungal Phytopathogen Magnaporthe oryzae

inferred← citeshttps://doi.org/10.1094/mpmi-34-11openalex-snapshot

Full Issue PDF

inferred← citeshttps://doi.org/10.1101/2020.12.17.423258openalex-snapshot

Genotype-phenotype map of an RNA-ligand complex

inferred← citeshttps://doi.org/10.1101/2020.12.17.423357openalex-snapshot

League of Brazilian Bioinformatics: a competition framework to promote scientific training

inferred← citeshttps://doi.org/10.1101/2022.08.06.503062openalex-snapshot

Interpretable RNA Foundation Model from Unannotated Data for Highly Accurate RNA Structure and Function Predictions

inferred← citeshttps://doi.org/10.1101/2022.10.10.510645openalex-snapshot

Publicly Available Privacy-preserving Benchmarks for Polygenic Prediction

inferred← citeshttps://doi.org/10.1101/2022.11.10.516002openalex-snapshot

FASSO: An AlphaFold based method to assign functional annotations by combining sequence and structure orthology

inferred← citeshttps://doi.org/10.1101/2022.11.17.516977openalex-snapshot

Exploration of the autonomous replication region and its utilization for expression vectors in cyanobacteria

inferred← citeshttps://doi.org/10.1101/2023.06.05.543750openalex-snapshot

Bench-ML: A Benchmarking Web Interface for Machine Learning Methods and Models in Genomics

inferred← citeshttps://doi.org/10.1101/2025.01.08.631847openalex-snapshot

Protein Structure Description with ρ, θ and ϕ : A Case Study with Caenopore-5

inferred← citeshttps://doi.org/10.1101/2025.02.11.637417openalex-snapshot

AI-qualizing Science

inferred← citeshttps://doi.org/10.1101/2025.07.18.665582openalex-snapshot

The Inaugural Flatiron Institute Cryo-EM Conformational Heterogeneity Challenge

inferred← citeshttps://doi.org/10.1101/677328openalex-snapshot

Using machine learning to predict quantitative phenotypes from protein and nucleic acid sequences

inferred← citeshttps://doi.org/10.1101/704874openalex-snapshot

UDSMProt: Universal Deep Sequence Models for Protein Classification

inferred← citeshttps://doi.org/10.1107/s2059798321007531openalex-snapshot

Protein structure prediction by AlphaFold 2: are attention and symmetries all you need?

inferred← citeshttps://doi.org/10.1107/s2059798322002157openalex-snapshot

The X-ray crystallography phase problem solved thanks to AlphaFold and RoseTTAFold models: a case-study report

inferred← citeshttps://doi.org/10.1109/acctcs53867.2022.00058openalex-snapshot

Investigation of Machine Learning Methods for Oxidation and Tensile Creep Properties of SiC/SiC Composites

inferred← citeshttps://doi.org/10.1109/aie57029.2022.00021openalex-snapshot

Deep Learning Methods For Prediction of HLA-Peptide Interactions in IDB

inferred← citeshttps://doi.org/10.1109/cccai59026.2023.00025openalex-snapshot

A benchmark study of protein folding algorithms on nanobodies

inferred← citeshttps://doi.org/10.1109/cibcb56990.2023.10264875openalex-snapshot

Neural Architecture Search for Genomic Sequence Data

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