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#TitleJournalYearCitations
1Basic local alignment search toolJournal of Molecular Biology199082,180
2Detection of specific sequences among DNA fragments separated by gel electrophoresisJournal of Molecular Biology197535,546
3A simple method for displaying the hydropathic character of a proteinJournal of Molecular Biology198222,171
4SHELXT– Integrated space-group and crystal-structure determinationActa Crystallographica Section A: Foundations and Advances201518,933
5WGCNA: an R package for weighted correlation network analysisBMC Bioinformatics200817,294
6RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genomeBMC Bioinformatics201116,042
7BLAST+: architecture and applicationsBMC Bioinformatics200914,935
8Labeling deoxyribonucleic acid to high specific activity in vitro by nick translation with DNA polymerase IJournal of Molecular Biology197713,093
9Comparative Protein Modelling by Satisfaction of Spatial RestraintsJournal of Molecular Biology199311,892
10A procedure for the isolation of deoxyribonucleic acid from micro-organismsJournal of Molecular Biology196111,512
11Predicting transmembrane protein topology with a hidden markov model: application to complete genomes11Edited by F. CohenJournal of Molecular Biology200111,404
12Basic Local Alignment Search ToolJournal of Molecular Biology199011,186
13Studies on transformation of Escherichia coli with plasmidsJournal of Molecular Biology198310,861
14A general method applicable to the search for similarities in the amino acid sequence of two proteinsJournal of Molecular Biology19709,639
15The protein data bank: A computer-based archival file for macromolecular structuresJournal of Molecular Biology19778,738
16pROC: an open-source package for R and S+ to analyze and compare ROC curvesBMC Bioinformatics20118,498
17Inference of Macromolecular Assemblies from Crystalline StateJournal of Molecular Biology20078,484
18On the nature of allosteric transitions: A plausible modelJournal of Molecular Biology19658,467
19Identification of common molecular subsequencesJournal of Molecular Biology19818,440
20Prodigal: prokaryotic gene recognition and translation initiation site identificationBMC Bioinformatics20108,237
21Solvent content of protein crystalsJournal of Molecular Biology19688,228
22GSVA: gene set variation analysis for microarray and RNA-Seq dataBMC Bioinformatics20137,876
23MUSCLE: a multiple sequence alignment method with reduced time and space complexityBMC Bioinformatics20047,508
24T-coffee: a novel method for fast and accurate multiple sequence alignment 1 1Edited by J. ThorntonJournal of Molecular Biology20006,404
25Selective extraction of polyoma DNA from infected mouse cell culturesJournal of Molecular Biology19676,287
26Use of bacteriophage T7 RNA polymerase to direct selective high-level expression of cloned genesJournal of Molecular Biology19866,199
27Comparison of multiple Amber force fields and development of improved protein backbone parametersProteins: Structure, Function and Bioinformatics20066,049
28Improved Prediction of Signal Peptides: SignalP 3.0Journal of Molecular Biology20046,015
29Genetic regulatory mechanisms in the synthesis of proteinsJournal of Molecular Biology19616,014
30Development and validation of a genetic algorithm for flexible docking 1 1Edited by F. E. CohenJournal of Molecular Biology19975,937
31An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein databaseJournal of the American Society for Mass Spectrometry19945,912
32The interpretation of protein structures: Estimation of static accessibilityJournal of Molecular Biology19715,785
33SCOP: a structural classification of proteins database for the investigation of sequences and structuresJournal of Molecular Biology19955,400
34Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbonsProteins: Structure, Function and Bioinformatics19915,360
35Enrichr: interactive and collaborative HTML5 gene list enrichment analysis toolBMC Bioinformatics20135,305
36Genome sequence-based species delimitation with confidence intervals and improved distance functionsBMC Bioinformatics20135,139
37Protein secondary structure prediction based on position-specific scoring matrices 1 1Edited by G. Von HeijneJournal of Molecular Biology19995,026
38Computer Visualization of Three-Dimensional Image Data Using IMODJournal of Structural Biology19964,964
39From FastQ Data to High‐Confidence Variant Calls: The Genome Analysis Toolkit Best Practices PipelineCurrent Protocols in Bioinformatics20134,796
40An automated method for finding molecular complexes in large protein interaction networksBMC Bioinformatics20034,773
41RELION: Implementation of a Bayesian approach to cryo-EM structure determinationJournal of Structural Biology20124,715
42Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteinsJournal of Molecular Biology19784,696
43Improved side‐chain torsion potentials for the Amber ff99SB protein force fieldProteins: Structure, Function and Bioinformatics20104,694
44ImageJ2: ImageJ for the next generation of scientific image dataBMC Bioinformatics20174,464
45Primer-BLAST: A tool to design target-specific primers for polymerase chain reactionBMC Bioinformatics20124,446
46Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperatureJournal of Molecular Biology19624,433
47I-TASSER server for protein 3D structure predictionBMC Bioinformatics20084,415
48Automated electron microscope tomography using robust prediction of specimen movementsJournal of Structural Biology20054,320
49A complementation analysis of the restriction and modification of DNA in Escherichia coliJournal of Molecular Biology19694,258
50Predicting Subcellular Localization of Proteins Based on their N-terminal Amino Acid SequenceJournal of Molecular Biology20004,166
51Structure validation by Cα geometry: ϕ,ψ and Cβ deviationProteins: Structure, Function and Bioinformatics20034,134
52Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in PhenixActa Crystallographica Section D: Structural Biology20194,060
53Maturation of the head of bacteriophage T4Journal of Molecular Biology19734,042
54Diffusion of univalent ions across the lamellae of swollen phospholipidsJournal of Molecular Biology19654,013
55Theoretical studies of enzymic reactions: Dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozymeJournal of Molecular Biology19763,971
56SCOP: A structural classification of proteins database for the investigation of sequences and structuresJournal of Molecular Biology19953,952
57The COG database: an updated version includes eukaryotesBMC Bioinformatics20033,913
58CTFFIND4: Fast and accurate defocus estimation from electron micrographsJournal of Structural Biology20153,894
59Protein Structure Comparison by Alignment of Distance MatricesJournal of Molecular Biology19933,851
60Cloning in single-stranded bacteriophage as an aid to rapid DNA sequencingJournal of Molecular Biology19803,786
61Prediction of complete gene structures in human genomic DNAJournal of Molecular Biology19973,746
62ViennaRNA Package 2.0Algorithms for Molecular Biology20113,719
63Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structureJournal of Molecular Biology19993,486
64cytoHubba: identifying hub objects and sub-networks from complex interactomeBMC Systems Biology20143,371
65Gctf: Real-time CTF determination and correctionJournal of Structural Biology20163,244
66The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomesBMC Bioinformatics20083,200
67Stereochemistry of polypeptide chain configurationsJournal of Molecular Biology19633,147
68Model for the structure of bacteriorhodopsin based on high-resolution electron cryo-microscopyJournal of Molecular Biology19903,109
69CpG Islands in vertebrate genomesJournal of Molecular Biology19873,038
70GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene listsBMC Bioinformatics20093,032
71MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile dataBMC Bioinformatics20103,031
72Essential dynamics of proteinsProteins: Structure, Function and Bioinformatics19932,927
73Theoretical aspects of DNA-protein interactions: Co-operative and non-co-operative binding of large ligands to a one-dimensional homogeneous latticeJournal of Molecular Biology19742,895
74BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome SequencesJournal of Molecular Biology20162,872
75Prediction of Protein Secondary Structure at Better than 70% AccuracyJournal of Molecular Biology19932,860
76Comparative Protein Structure Modeling Using ModellerCurrent Protocols in Bioinformatics20062,858
77The CCPN data model for NMR spectroscopy: Development of a software pipelineProteins: Structure, Function and Bioinformatics20052,805
78EMAN2: An extensible image processing suite for electron microscopyJournal of Structural Biology20072,798
79Sequence and structure-based prediction of eukaryotic protein phosphorylation sitesJournal of Molecular Biology19992,767
80Calcium-dependent bacteriophage DNA infectionJournal of Molecular Biology19702,741
81Torsion angle dynamics for NMR structure calculation with the new program DyanaJournal of Molecular Biology19972,731
82Reagent and laboratory contamination can critically impact sequence-based microbiome analysesBMC Biology20142,677
83Intrinsically unstructured proteins: re-assessing the protein structure-function paradigmJournal of Molecular Biology19992,668
84Analysis of gene control signals by DNA fusion and cloning in Escherichia coliJournal of Molecular Biology19802,655
85A Fast Flexible Docking Method using an Incremental Construction AlgorithmJournal of Molecular Biology19962,609
86DNA methylation arrays as surrogate measures of cell mixture distributionBMC Bioinformatics20122,563
87Molecular dynamics simulations of biomoleculesNature Structural Biology20022,473
88Gene finding in novel genomesBMC Bioinformatics20042,443
89Improved protein-ligand docking using GOLDProteins: Structure, Function and Bioinformatics20032,417
90Funnels, pathways, and the energy landscape of protein folding: A synthesisProteins: Structure, Function and Bioinformatics19952,415
91The GeneCards Suite: From Gene Data Mining to Disease Genome Sequence AnalysesCurrent Protocols in Bioinformatics20162,405
92Analysis of bacteriophage T7 early RNAs and proteins on slab gelsJournal of Molecular Biology19732,380
93‘Green mice’ as a source of ubiquitous green cellsFEBS Letters19972,364
94Announcing the worldwide Protein Data BankNature Structural and Molecular Biology20032,355
95CATH – a hierarchic classification of protein domain structuresStructure19972,347
96Exon-intron circular RNAs regulate transcription in the nucleusNature Structural and Molecular Biology20152,330
97Sedimentation studies of the size and shape of DNAJournal of Molecular Biology19652,329
98Automated protein model building combined with iterative structure refinementNature Structural Biology19992,328
99Bias in random forest variable importance measures: Illustrations, sources and a solutionBMC Bioinformatics20072,328
100EMAN: Semiautomated Software for High-Resolution Single-Particle ReconstructionsJournal of Structural Biology19992,320