Research graph
References from Big data enabled discovery in bioinformatics and structural biology. Local targets link to admitted publications; unresolved targets remain external evidence.
A brief survey on big data: technologies, terminologies and data-intensive applications
10.1186/s40537-022-00659-3 · 2022 · External reference
The galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update
10.1093/nar/gkae410 · 2024 · External reference
Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the protein data bank (PDB)
10.1107/s2059798319004522 · 2019 · External reference
Graph-based methods for analysing networks in cell biology
10.1093/bib/bbl022 · 2006 · External reference
Comparison of linear and nonlinear calibration models based on near infrared (NIR) spectroscopy data for gasoline properties prediction
10.1016/j.chemolab.2007.04.006 · 2007 · External reference
Quantifying and managing uncertainty in systems biology: mechanistic and data-driven models
10.1016/j.coisb.2025.100557 · 2025 · External reference
Clustering predicted structures at the scale of the known protein universe
10.1038/s41586-023-06510-w · 2023 · External reference
Jian Zhang, uniprot: the universal protein knowledgebase in 2023
10.1093/nar/gkac1052 · 2023 · External reference
Computational biology in the 21st century: scaling with compressive algorithms
10.1145/2957324 · 2016 · External reference
Protein data bank (PDB): fifty-three years young and having a transformative impact on science and society
10.1017/s0033583525000034 · 2025 · External reference
MMTF—An efficient file format for the transmission, visualization, and analysis of macromolecular structures
10.1371/journal.pcbi.1005575 · 2017 · External reference
Protein data bank: a comprehensive review of 3D structure holdings and worldwide utilization by researchers, educators, and students
10.3390/biom12101425 · 2022 · External reference
NAPS: network analysis of protein structures
10.1093/nar/gkw383 · 2016 · External reference
Protein bioinformatics infrastructure for the integration and analysis of multiple high-throughput omics data
10.1155/2010/423589 · 2010 · External reference
Nonlinear discovery of slow molecular modes using state-free reversible VAMPnets
10.1063/1.5092521 · 2019 · External reference
Enhanced sampling for efficient learning of coarse-grained machine learning potentials
10.1021/acs.jctc.5c01712 · 2026 · External reference
MRC2014: extensions to the MRC format header for electron cryo-microscopy and tomography
10.1016/j.jsb.2015.04.002 · 2015 · External reference
Chapter 5: network biology approach to complex diseases
10.1371/journal.pcbi.1002820 · 2012 · External reference
PDB NextGen Archive: centralizing access to integrated annotations and enriched structural information by the Worldwide Protein Data Bank
10.1093/database/baae041 · 2024 · External reference
The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants
10.1093/nar/gkp1137 · 2009 · External reference
EnGens: a computational framework for generation and analysis of representative protein conformational ensembles
10.1093/bib/bbad242 · 2023 · External reference
Network propagation: a universal amplifier of genetic associations
10.1038/nrg.2017.38 · 2017 · External reference
Pathway and network analysis of cancer genomes
10.1038/nmeth.3440 · 2015 · External reference
MRC image processing programs
10.1006/jsbi.1996.0003 · 1996 · External reference
Exploring the potential of 3D Zernike descriptors and SVM for protein-protein interface prediction
10.1186/s12859-018-2043-3 · 2018 · External reference
The variant call format and VCFtools
2011 · External reference
Unresolved reference
1990 · External reference
Challenges of big data integration in the life sciences
10.1007/s00216-019-02074-9 · 2019 · External reference
10.1145/1966895.1966900
10.1145/1966895.1966900 · External reference
Values, challenges and future directions of big data analytics in healthcare: a systematic review
10.1016/j.socscimed.2019.112533 · 2019 · External reference
Chapter eight - biological big data analytics
10.1016/bs.adcom.2017.08.002 · 2018 · External reference
The reactome pathway knowledgebase 2022
10.1093/nar/gkab1028 · 2022 · External reference
PDBeCIF: an open-source mmCIF/CIF parsing and processing package
10.1186/s12859-021-04271-9 · 2021 · External reference
Unsupervised learning methods for molecular simulation data
10.1021/acs.chemrev.0c01195 · 2021 · External reference
Big data bioinformatics
10.1002/jcp.24662 · 2014 · External reference
The importance of data compression in the field of genomics
10.1109/mpuls.2019.2899747 · 2019 · External reference
Addressing big data challenges in mass spectrometry-based metabolomics
10.1039/d2cc03598g · 2022 · External reference
Big data in bioinformatics and computational biology: basic insights
10.1007/978-1-0716-3461-5_9 · 2024 · External reference
The challenges of explainable AI in biomedical data science
2022 · External reference
A global map of the protein shape universe
10.1371/journal.pcbi.1006969 · 2019 · External reference
Jmol – a paradigm shift in crystallographic visualization
10.1107/s0021889810030256 · 2010 · External reference
Big data analytics for genomic medicine
10.3390/ijms18020412 · 2017 · External reference
Bilingual language model for protein sequence and structure
10.1093/nargab/lqae150 · 2024 · External reference
Introduction of the Capsules environment to support further growth of the SBGrid structural biology software collection
10.1107/s2059798324004881 · 2024 · External reference
Bringing molecular dynamics simulation data into view
10.1016/j.tibs.2019.06.004 · 2019 · External reference
Biological magnetic resonance data bank
10.1093/nar/gkac1050 · 2023 · External reference
Knowledge discovery and interactive data mining in bioinformatics - state-of-the-art, future challenges and research directions
2014 · External reference
RR3DD: an RNA global structure-based RNA three-dimensional structural classification database
10.1080/15476286.2021.1989200 · 2021 · External reference
ConSole: using modularity of contact maps to locate solenoid domains in protein structures
10.1186/1471-2105-15-119 · 2014 · External reference
VMD: visual molecular dynamics
10.1016/0263-7855(96)00018-5 · 1996 · External reference
EMPIAR: the electron microscopy public image archive
10.1093/nar/gkac1062 · 2023 · External reference
Editorial: hybrid biomolecular modeling
10.3389/fmolb.2018.00098 · 2018 · External reference
Highly accurate protein structure prediction with AlphaFold
10.1038/s41586-021-03819-2 · 2021 · External reference
Uap: reproducible and robust HTS data analysis
10.1186/s12859-019-3219-1 · 2019 · External reference
The DBCLS biohackathon: standardization and interoperability for bioinformatics web services and workflows
10.1186/2041-1480-1-8 · 2010 · External reference
BigWig and BigBed: enabling browsing of large distributed datasets
2010 · External reference
The human genome browser at UCSC
10.1101/gr.229102 · 2002 · External reference
Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks
10.1038/s41467-021-27222-7 · 2021 · External reference
Deep learning in structural bioinformatics: current applications and future perspectives
10.1093/bib/bbae042 · 2024 · External reference
Dockground: a comprehensive data resource for modeling of protein complexes
10.1002/pro.3295 · 2018 · External reference
Structural biology in cellulo: minding the gap between conceptualization and realization
10.1016/j.sbi.2024.102843 · 2024 · External reference
CHARMM-GUI input generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM simulations using the CHARMM36 additive force field
10.1021/acs.jctc.5b00935 · 2016 · External reference
The sequence alignment/map format and SAMtools
2009 · External reference
Progress and opportunities of foundation models in bioinformatics
10.1093/bib/bbae548 · 2024 · External reference
Big biological data: challenges and opportunities
10.1016/j.gpb.2014.10.001 · 2014 · External reference
Evolutionary-scale prediction of atomic-level protein structure with a language model
10.1126/science.ade2574 · 2023 · External reference
BindingDB in 2024: a FAIR knowledgebase of protein-small molecule binding data
10.1093/nar/gkae1075 · 2025 · External reference
Integrated bio-search: challenges and trends for the integration, search and comprehensive processing of biological information
10.1186/1471-2105-15-s1-s2 · 2014 · External reference
An evaluation of human protein-protein interaction data in the public domain
2006 · External reference
MDTraj: a modern open library for the analysis of molecular dynamics trajectories
10.1016/j.bpj.2015.08.015 · 2015 · External reference
Challenges and limitations of biological network analysis
10.3390/biotech11030024 · 2022 · External reference
Uniclust databases of clustered and deeply annotated protein sequences and alignments
10.1093/nar/gkw1081 · 2017 · External reference
An overview of microcrystal electron diffraction (MicroED)
10.1146/annurev-biochem-081720-020121 · 2021 · External reference
The real cost of sequencing: scaling computation to keep pace with data generation
2016 · External reference
Assessing and assuring interoperability of a genomics file format
2022 · External reference
The complete sequence of a human genome
10.1126/science.abj6987 · 2022 · External reference
Integrative multi-omics and systems bioinformatics in translational neuroscience: a data mining perspective
10.1016/j.jpha.2023.06.011 · 2023 · External reference
Databases of protein-protein interactions and complexes
10.1007/978-1-60327-241-4_9 · 2010 · External reference
The BioGRID database: a comprehensive biomedical resource of curated protein, genetic, and chemical interactions
10.1002/pro.3978 · 2021 · External reference
Accelerating genomic workflows using NVIDIA Parabricks
10.1186/s12859-023-05292-2 · 2023 · External reference
Small data, big challenges: machine- and deep-learning strategies for data-limited drug discovery
10.1016/j.addr.2025.115762 · 2026 · External reference
Improved tools for biological sequence comparison
10.1073/pnas.85.8.2444 · 1988 · External reference
Semi-supervised learning with pseudo-labeling compares favorably with large language models for regulatory sequence prediction
10.1093/bib/bbae560 · 2024 · External reference
Querying large read collections in main memory: a versatile data structure
10.1186/1471-2105-12-242 · 2011 · External reference
Big data in contemporary electron microscopy: challenges and opportunities in data transfer, compute and management
10.1007/s00418-023-02191-8 · 2023 · External reference
Bioinformatics and the developing world
1999 · External reference
BEDTools: a flexible suite of utilities for comparing genomic features
2010 · External reference
3Dmol.js: molecular visualization with WebGL
2015 · External reference
Pathway enrichment analysis and visualization of omics data using g:profiler, GSEA, Cytoscape and EnrichmentMap
10.1038/s41596-018-0103-9 · 2019 · External reference
Machine learning approaches for biomolecular, biophysical, and biomaterials research
10.1063/5.0082179 · 2022 · External reference
PTRAJ and CPPTRAJ: software for processing and analysis of molecular dynamics trajectory data
10.1021/ct400341p · 2013 · External reference
NGL viewer: a web application for molecular visualization
10.1093/nar/gkv402 · 2015 · External reference
NGL viewer: web-based molecular graphics for large complexes
2018 · External reference
Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy
10.1016/j.jmb.2003.07.013 · 2003 · External reference
Fast protein tertiary structure retrieval based on global surface shape similarity
10.1002/prot.22030 · 2008 · External reference
From integrative structural biology to cell biology
10.1016/j.jbc.2021.100743 · 2021 · External reference
Modeling biological complexes using integrative modeling platform
10.1007/978-1-4939-9608-7_15 · 2019 · External reference
Current progress and open challenges for applying deep learning across the biosciences
10.1038/s41467-022-29268-7 · 2022 · External reference
Database resources of the national center for biotechnology information in 2023
10.1093/nar/gkac1032 · 2023 · External reference
PyEMMA 2: a software package for estimation, validation, and analysis of markov models
10.1021/acs.jctc.5b00743 · 2015 · External reference
NmrML: a community supported open data standard for the description, storage, and exchange of NMR data
10.1021/acs.analchem.7b02795 · 2018 · External reference
The future of integrated structural biology
10.1016/j.str.2024.08.014 · 2024 · External reference
Modeling molecular kinetics with tICA and the kernel trick
10.1021/ct5007357 · 2015 · External reference
LiteMol suite: interactive web-based visualization of large-scale macromolecular structure data
10.1038/nmeth.4499 · 2017 · External reference
BinaryCIF and CIFTools—Lightweight, efficient and extensible macromolecular data management
10.1371/journal.pcbi.1008247 · 2020 · External reference
Mol∗Viewer: modern web app for 3D visualization and analysis of large biomolecular structures
10.1093/nar/gkab314 · 2021 · External reference
Accurate RNA 3D structure prediction using a language model-based deep learning approach
10.1038/s41592-024-02487-0 · 2024 · External reference
The importance, challenges, and possible solutions for sharing proteomics data while safeguarding individuals' privacy
10.1016/j.mcpro.2024.100731 · 2024 · External reference
Guo, InteracTor: feature engineering and explainable AI for profiling protein structure-interaction-function relationships
10.1371/journal.pcbi.1013038 · 2025 · External reference
Network medicine in the age of biomedical big data
10.3389/fgene.2019.00294 · 2019 · External reference
RNAcentral 2021: secondary structure integration, improved sequence search and new member databases
10.1093/nar/gkaa921 · 2021 · External reference
The STRING database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest
10.1093/nar/gkac1000 · 2023 · External reference
Application of a modular feedforward neural network for grade estimation
10.1007/s11053-011-9135-3 · 2011 · External reference
UniProt: a hub for protein information
10.1093/nar/gku989 · 2015 · External reference
MDverse, shedding light on the dark matter of molecular dynamics simulations
10.7554/elife.90061.3.sa4 · 2024 · External reference
The IntAct database: efficient access to fine-grained molecular interaction data
10.1093/nar/gkab1006 · 2022 · External reference
PLUMED Tutorials: a collaborative, community-driven learning ecosystem
10.1063/5.0251501 · 2025 · External reference
UMAP as a dimensionality reduction tool for molecular dynamics simulations of biomacromolecules: a comparison study
10.1021/acs.jpcb.1c02081 · 2021 · External reference
Highly accurate protein structure prediction for the human proteome
10.1038/s41586-021-03828-1 · 2021 · External reference
Xiaodan Ma, EMDB—the electron microscopy data bank
10.1093/nar/gkad1019 · 2024 · External reference
NMR-STAR: comprehensive ontology for representing, archiving and exchanging data from nuclear magnetic resonance spectroscopic experiments
10.1007/s10858-018-0220-3 · 2019 · External reference
SASBDB, a repository for biological small-angle scattering data
10.1093/nar/gku1047 · 2015 · External reference
ModelCIF: an extension of PDBx/mmCIF data representation for computed structure models
10.1016/j.jmb.2023.168021 · 2023 · 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
AlphaFold protein structure database in 2024: providing structure coverage for over 214 million protein sequences
10.1093/nar/gkad1011 · 2024 · External reference
Everything is connected: graph neural networks
10.1016/j.sbi.2023.102538 · 2023 · External reference
Semantic data integration of big biomedical data for supporting personalised medicine
2019 · External reference
Reprogramming pretrained language models for protein sequence representation learning
10.1039/d4dd00195h · 2025 · External reference
Big data privacy in biomedical research
10.1109/tbdata.2016.2608848 · 2020 · External reference
Modeling bias toward binding sites in PDB structural models
2024 · External reference
Ten rules for a structural bioinformatic analysis
10.1371/journal.pcbi.1013094 · 2025 · External reference
The application of convolutional neural networks (CNNs) to recognize defects in 3D-printed parts
10.3390/ma14102575 · 2021 · External reference
The PDB format, mmCIF, and other data formats.
2003 · External reference
PDBx/mmCIF ecosystem: foundational semantic tools for structural biology
10.1016/j.jmb.2022.167599 · 2022 · External reference
Temporal and spatial dynamics of scaling-specific features of a gene regulatory network in Drosophila
10.1038/ncomms10031 · 2015 · External reference
Deep learning in bioinformatics
10.55730/1300-0152.2671 · 2023 · External reference
Graphery: interactive tutorials for biological network algorithms
10.1093/nar/gkab420 · 2021 · External reference
PDC: a highly compact file format to store protein 3D coordinates
10.1093/database/baad018 · 2023 · External reference
Machine learning for integrating data in biology and medicine: principles, practice, and opportunities
10.1016/j.inffus.2018.09.012 · 2019 · External reference
Big data bioinformatics
10.1002/jcp.24662 · ExternalCitation · doi-reference
Dockground: a comprehensive data resource for modeling of protein complexes
10.1002/pro.3295 · ExternalCitation · doi-reference
The BioGRID database: a comprehensive biomedical resource of curated protein, genetic, and chemical interactions
10.1002/pro.3978 · ExternalCitation · doi-reference
Fast protein tertiary structure retrieval based on global surface shape similarity
10.1002/prot.22030 · ExternalCitation · doi-reference
MRC image processing programs
10.1006/jsbi.1996.0003 · ExternalCitation · doi-reference
Big data in bioinformatics and computational biology: basic insights
10.1007/978-1-0716-3461-5_9 · ExternalCitation · doi-reference
Modeling biological complexes using integrative modeling platform
10.1007/978-1-4939-9608-7_15 · ExternalCitation · doi-reference
Databases of protein-protein interactions and complexes
10.1007/978-1-60327-241-4_9 · ExternalCitation · doi-reference
Challenges of big data integration in the life sciences
10.1007/s00216-019-02074-9 · ExternalCitation · doi-reference
Big data in contemporary electron microscopy: challenges and opportunities in data transfer, compute and management
10.1007/s00418-023-02191-8 · ExternalCitation · doi-reference
NMR-STAR: comprehensive ontology for representing, archiving and exchanging data from nuclear magnetic resonance spectroscopic experiments
10.1007/s10858-018-0220-3 · ExternalCitation · doi-reference
Application of a modular feedforward neural network for grade estimation
10.1007/s11053-011-9135-3 · ExternalCitation · doi-reference
VMD: visual molecular dynamics
10.1016/0263-7855(96)00018-5 · ExternalCitation · doi-reference
Chapter eight - biological big data analytics
10.1016/bs.adcom.2017.08.002 · ExternalCitation · doi-reference
Small data, big challenges: machine- and deep-learning strategies for data-limited drug discovery
10.1016/j.addr.2025.115762 · ExternalCitation · doi-reference
MDTraj: a modern open library for the analysis of molecular dynamics trajectories
10.1016/j.bpj.2015.08.015 · ExternalCitation · doi-reference
Comparison of linear and nonlinear calibration models based on near infrared (NIR) spectroscopy data for gasoline properties prediction
10.1016/j.chemolab.2007.04.006 · ExternalCitation · doi-reference
Quantifying and managing uncertainty in systems biology: mechanistic and data-driven models
10.1016/j.coisb.2025.100557 · ExternalCitation · doi-reference
Big biological data: challenges and opportunities
10.1016/j.gpb.2014.10.001 · ExternalCitation · doi-reference
Machine learning for integrating data in biology and medicine: principles, practice, and opportunities
10.1016/j.inffus.2018.09.012 · ExternalCitation · doi-reference
From integrative structural biology to cell biology
10.1016/j.jbc.2021.100743 · ExternalCitation · doi-reference
Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy
10.1016/j.jmb.2003.07.013 · ExternalCitation · doi-reference
PDBx/mmCIF ecosystem: foundational semantic tools for structural biology
10.1016/j.jmb.2022.167599 · ExternalCitation · doi-reference
ModelCIF: an extension of PDBx/mmCIF data representation for computed structure models
10.1016/j.jmb.2023.168021 · ExternalCitation · doi-reference
Integrative multi-omics and systems bioinformatics in translational neuroscience: a data mining perspective
10.1016/j.jpha.2023.06.011 · ExternalCitation · doi-reference
MRC2014: extensions to the MRC format header for electron cryo-microscopy and tomography
10.1016/j.jsb.2015.04.002 · ExternalCitation · doi-reference
The importance, challenges, and possible solutions for sharing proteomics data while safeguarding individuals' privacy
10.1016/j.mcpro.2024.100731 · ExternalCitation · doi-reference
Everything is connected: graph neural networks
10.1016/j.sbi.2023.102538 · ExternalCitation · doi-reference
Structural biology in cellulo: minding the gap between conceptualization and realization
10.1016/j.sbi.2024.102843 · ExternalCitation · doi-reference
Values, challenges and future directions of big data analytics in healthcare: a systematic review
10.1016/j.socscimed.2019.112533 · ExternalCitation · doi-reference
The future of integrated structural biology
10.1016/j.str.2024.08.014 · ExternalCitation · doi-reference
Bringing molecular dynamics simulation data into view
10.1016/j.tibs.2019.06.004 · ExternalCitation · doi-reference
Protein data bank (PDB): fifty-three years young and having a transformative impact on science and society
10.1017/s0033583525000034 · ExternalCitation · doi-reference
NmrML: a community supported open data standard for the description, storage, and exchange of NMR data
10.1021/acs.analchem.7b02795 · ExternalCitation · doi-reference
Unsupervised learning methods for molecular simulation data
10.1021/acs.chemrev.0c01195 · ExternalCitation · doi-reference
PyEMMA 2: a software package for estimation, validation, and analysis of markov models
10.1021/acs.jctc.5b00743 · ExternalCitation · doi-reference
CHARMM-GUI input generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM simulations using the CHARMM36 additive force field
10.1021/acs.jctc.5b00935 · ExternalCitation · doi-reference
Enhanced sampling for efficient learning of coarse-grained machine learning potentials
10.1021/acs.jctc.5c01712 · ExternalCitation · doi-reference
UMAP as a dimensionality reduction tool for molecular dynamics simulations of biomacromolecules: a comparison study
10.1021/acs.jpcb.1c02081 · ExternalCitation · doi-reference
PTRAJ and CPPTRAJ: software for processing and analysis of molecular dynamics trajectory data
10.1021/ct400341p · ExternalCitation · doi-reference
Modeling molecular kinetics with tICA and the kernel trick
10.1021/ct5007357 · ExternalCitation · doi-reference
Temporal and spatial dynamics of scaling-specific features of a gene regulatory network in Drosophila
10.1038/ncomms10031 · ExternalCitation · doi-reference
Pathway and network analysis of cancer genomes
10.1038/nmeth.3440 · ExternalCitation · doi-reference
LiteMol suite: interactive web-based visualization of large-scale macromolecular structure data
10.1038/nmeth.4499 · ExternalCitation · doi-reference
Network propagation: a universal amplifier of genetic associations
10.1038/nrg.2017.38 · ExternalCitation · doi-reference
Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks
10.1038/s41467-021-27222-7 · ExternalCitation · doi-reference
Current progress and open challenges for applying deep learning across the biosciences
10.1038/s41467-022-29268-7 · 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
Clustering predicted structures at the scale of the known protein universe
10.1038/s41586-023-06510-w · ExternalCitation · doi-reference
Accurate RNA 3D structure prediction using a language model-based deep learning approach
10.1038/s41592-024-02487-0 · ExternalCitation · doi-reference
Pathway enrichment analysis and visualization of omics data using g:profiler, GSEA, Cytoscape and EnrichmentMap
10.1038/s41596-018-0103-9 · ExternalCitation · doi-reference
Addressing big data challenges in mass spectrometry-based metabolomics
10.1039/d2cc03598g · ExternalCitation · doi-reference
Reprogramming pretrained language models for protein sequence representation learning
10.1039/d4dd00195h · ExternalCitation · doi-reference
Nonlinear discovery of slow molecular modes using state-free reversible VAMPnets
10.1063/1.5092521 · ExternalCitation · doi-reference
Machine learning approaches for biomolecular, biophysical, and biomaterials research
10.1063/5.0082179 · ExternalCitation · doi-reference
PLUMED Tutorials: a collaborative, community-driven learning ecosystem
10.1063/5.0251501 · ExternalCitation · doi-reference
Improved tools for biological sequence comparison
10.1073/pnas.85.8.2444 · ExternalCitation · doi-reference
RR3DD: an RNA global structure-based RNA three-dimensional structural classification database
10.1080/15476286.2021.1989200 · ExternalCitation · doi-reference
EnGens: a computational framework for generation and analysis of representative protein conformational ensembles
10.1093/bib/bbad242 · ExternalCitation · doi-reference
Deep learning in structural bioinformatics: current applications and future perspectives
10.1093/bib/bbae042 · ExternalCitation · doi-reference
Progress and opportunities of foundation models in bioinformatics
10.1093/bib/bbae548 · ExternalCitation · doi-reference
Semi-supervised learning with pseudo-labeling compares favorably with large language models for regulatory sequence prediction
10.1093/bib/bbae560 · ExternalCitation · doi-reference
Graph-based methods for analysing networks in cell biology
10.1093/bib/bbl022 · ExternalCitation · doi-reference
PDC: a highly compact file format to store protein 3D coordinates
10.1093/database/baad018 · ExternalCitation · doi-reference
PDB NextGen Archive: centralizing access to integrated annotations and enriched structural information by the Worldwide Protein Data Bank
10.1093/database/baae041 · ExternalCitation · doi-reference
RNAcentral 2021: secondary structure integration, improved sequence search and new member databases
10.1093/nar/gkaa921 · ExternalCitation · doi-reference
The IntAct database: efficient access to fine-grained molecular interaction data
10.1093/nar/gkab1006 · ExternalCitation · doi-reference
The reactome pathway knowledgebase 2022
10.1093/nar/gkab1028 · 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
Mol∗Viewer: modern web app for 3D visualization and analysis of large biomolecular structures
10.1093/nar/gkab314 · ExternalCitation · doi-reference
Graphery: interactive tutorials for biological network algorithms
10.1093/nar/gkab420 · ExternalCitation · doi-reference
The STRING database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest
10.1093/nar/gkac1000 · ExternalCitation · doi-reference
Database resources of the national center for biotechnology information in 2023
10.1093/nar/gkac1032 · ExternalCitation · doi-reference
Biological magnetic resonance data bank
10.1093/nar/gkac1050 · ExternalCitation · doi-reference
Jian Zhang, uniprot: the universal protein knowledgebase in 2023
10.1093/nar/gkac1052 · ExternalCitation · doi-reference
EMPIAR: the electron microscopy public image archive
10.1093/nar/gkac1062 · ExternalCitation · doi-reference
AlphaFold protein structure database in 2024: providing structure coverage for over 214 million protein sequences
10.1093/nar/gkad1011 · ExternalCitation · doi-reference
Xiaodan Ma, EMDB—the electron microscopy data bank
10.1093/nar/gkad1019 · ExternalCitation · doi-reference
BindingDB in 2024: a FAIR knowledgebase of protein-small molecule binding data
10.1093/nar/gkae1075 · ExternalCitation · doi-reference
The galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update
10.1093/nar/gkae410 · ExternalCitation · doi-reference
The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants
10.1093/nar/gkp1137 · ExternalCitation · doi-reference
SASBDB, a repository for biological small-angle scattering data
10.1093/nar/gku1047 · ExternalCitation · doi-reference
UniProt: a hub for protein information
10.1093/nar/gku989 · ExternalCitation · doi-reference
NGL viewer: a web application for molecular visualization
10.1093/nar/gkv402 · ExternalCitation · doi-reference
Uniclust databases of clustered and deeply annotated protein sequences and alignments
10.1093/nar/gkw1081 · ExternalCitation · doi-reference
NAPS: network analysis of protein structures
10.1093/nar/gkw383 · ExternalCitation · doi-reference
Bilingual language model for protein sequence and structure
10.1093/nargab/lqae150 · ExternalCitation · doi-reference
The human genome browser at UCSC
10.1101/gr.229102 · ExternalCitation · doi-reference
Jmol – a paradigm shift in crystallographic visualization
10.1107/s0021889810030256 · ExternalCitation · doi-reference
Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the protein data bank (PDB)
10.1107/s2059798319004522 · ExternalCitation · doi-reference
Introduction of the Capsules environment to support further growth of the SBGrid structural biology software collection
10.1107/s2059798324004881 · ExternalCitation · doi-reference
The importance of data compression in the field of genomics
10.1109/mpuls.2019.2899747 · ExternalCitation · doi-reference
Big data privacy in biomedical research
10.1109/tbdata.2016.2608848 · ExternalCitation · doi-reference
The complete sequence of a human genome
10.1126/science.abj6987 · ExternalCitation · doi-reference
Evolutionary-scale prediction of atomic-level protein structure with a language model
10.1126/science.ade2574 · ExternalCitation · doi-reference
10.1145/1966895.1966900
10.1145/1966895.1966900 · ExternalCitation · doi-reference
Computational biology in the 21st century: scaling with compressive algorithms
10.1145/2957324 · ExternalCitation · doi-reference
An overview of microcrystal electron diffraction (MicroED)
10.1146/annurev-biochem-081720-020121 · ExternalCitation · doi-reference
Protein bioinformatics infrastructure for the integration and analysis of multiple high-throughput omics data
10.1155/2010/423589 · ExternalCitation · doi-reference
Querying large read collections in main memory: a versatile data structure
10.1186/1471-2105-12-242 · ExternalCitation · doi-reference
ConSole: using modularity of contact maps to locate solenoid domains in protein structures
10.1186/1471-2105-15-119 · ExternalCitation · doi-reference
Integrated bio-search: challenges and trends for the integration, search and comprehensive processing of biological information
10.1186/1471-2105-15-s1-s2 · ExternalCitation · doi-reference
The DBCLS biohackathon: standardization and interoperability for bioinformatics web services and workflows
10.1186/2041-1480-1-8 · ExternalCitation · doi-reference
Exploring the potential of 3D Zernike descriptors and SVM for protein-protein interface prediction
10.1186/s12859-018-2043-3 · ExternalCitation · doi-reference
Uap: reproducible and robust HTS data analysis
10.1186/s12859-019-3219-1 · ExternalCitation · doi-reference
PDBeCIF: an open-source mmCIF/CIF parsing and processing package
10.1186/s12859-021-04271-9 · ExternalCitation · doi-reference
Accelerating genomic workflows using NVIDIA Parabricks
10.1186/s12859-023-05292-2 · ExternalCitation · doi-reference
A brief survey on big data: technologies, terminologies and data-intensive applications
10.1186/s40537-022-00659-3 · ExternalCitation · doi-reference
Chapter 5: network biology approach to complex diseases
10.1371/journal.pcbi.1002820 · ExternalCitation · doi-reference
MMTF—An efficient file format for the transmission, visualization, and analysis of macromolecular structures
10.1371/journal.pcbi.1005575 · ExternalCitation · doi-reference
A global map of the protein shape universe
10.1371/journal.pcbi.1006969 · ExternalCitation · doi-reference
BinaryCIF and CIFTools—Lightweight, efficient and extensible macromolecular data management
10.1371/journal.pcbi.1008247 · ExternalCitation · doi-reference
Guo, InteracTor: feature engineering and explainable AI for profiling protein structure-interaction-function relationships
10.1371/journal.pcbi.1013038 · ExternalCitation · doi-reference
Ten rules for a structural bioinformatic analysis
10.1371/journal.pcbi.1013094 · ExternalCitation · doi-reference
Network medicine in the age of biomedical big data
10.3389/fgene.2019.00294 · ExternalCitation · doi-reference
Editorial: hybrid biomolecular modeling
10.3389/fmolb.2018.00098 · ExternalCitation · doi-reference
Protein data bank: a comprehensive review of 3D structure holdings and worldwide utilization by researchers, educators, and students
10.3390/biom12101425 · ExternalCitation · doi-reference
Challenges and limitations of biological network analysis
10.3390/biotech11030024 · ExternalCitation · doi-reference
Big data analytics for genomic medicine
10.3390/ijms18020412 · ExternalCitation · doi-reference
The application of convolutional neural networks (CNNs) to recognize defects in 3D-printed parts
10.3390/ma14102575 · ExternalCitation · doi-reference
Deep learning in bioinformatics
10.55730/1300-0152.2671 · ExternalCitation · doi-reference
MDverse, shedding light on the dark matter of molecular dynamics simulations
10.7554/elife.90061.3.sa4 · ExternalCitation · doi-reference
