| # | Title | Journal | Year | Citations |
|---|
|
| 1 | GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers | SoftwareX | 2015 | 15,992 |
| 2 | Tissue-based map of the human proteome | Science | 2015 | 11,537 |
| 3 | SignalP 4.0: discriminating signal peptides from transmembrane regions | Nature Methods | 2011 | 8,661 |
| 4 | GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit | Bioinformatics | 2013 | 6,295 |
| 5 | MultiQC: summarize analysis results for multiple tools and samples in a single report | Bioinformatics | 2016 | 5,410 |
| 6 | New tools for automated high-resolution cryo-EM structure determination in RELION-3 | ELife | 2018 | 4,280 |
| 7 | The Pfam protein families database in 2019 | Nucleic Acids Research | 2019 | 4,133 |
| 8 | Infrared spectroscopy of proteins | Biochimica Et Biophysica Acta - Bioenergetics | 2007 | 3,710 |
| 9 | Pfam: The protein families database in 2021 | Nucleic Acids Research | 2021 | 3,647 |
| 10 | SignalP 5.0 improves signal peptide predictions using deep neural networks | Nature Biotechnology | 2019 | 3,566 |
| 11 | The Pfam protein families database | Nucleic Acids Research | 2012 | 3,364 |
| 12 | What vibrations tell about proteins | Quarterly Reviews of Biophysics | 2002 | 1,791 |
| 13 | The Norway spruce genome sequence and conifer genome evolution | Nature | 2013 | 1,339 |
| 14 | The nf-core framework for community-curated bioinformatics pipelines | Nature Biotechnology | 2020 | 1,322 |
| 15 | SignalP 6.0 predicts all five types of signal peptides using protein language models | Nature Biotechnology | 2022 | 1,142 |
| 16 | Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2 | ELife | 2016 | 936 |
| 17 | Implementation of the CHARMM Force Field in GROMACS: Analysis of Protein Stability Effects from Correction Maps, Virtual Interaction Sites, and Water Models | Journal of Chemical Theory and Computation | 2010 | 928 |
| 18 | Recognition of transmembrane helices by the endoplasmic reticulum translocon | Nature | 2005 | 908 |
| 19 | Metabolism and function of coenzyme Q | Biochimica Et Biophysica Acta - Biomembranes | 2004 | 880 |
| 20 | The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides | Nucleic Acids Research | 2015 | 816 |
| 21 | Mechanisms of Cellular Uptake of Cell-Penetrating Peptides | Journal of Biophysics | 2011 | 772 |
| 22 | Thermofluor-based high-throughput stability optimization of proteins for structural studies | Analytical Biochemistry | 2006 | 746 |
| 23 | In situ sequencing for RNA analysis in preserved tissue and cells | Nature Methods | 2013 | 720 |
| 24 | Assessment of transcript reconstruction methods for RNA-seq | Nature Methods | 2013 | 698 |
| 25 | Molecular code for transmembrane-helix recognition by the Sec61 translocon | Nature | 2007 | 658 |
| 26 | Detecting sequence signals in targeting peptides using deep learning | Life Science Alliance | 2019 | 637 |
| 27 | The amyloid β-peptide is imported into mitochondria via the TOM import machinery and localized to mitochondrial cristae | Proceedings of the National Academy of Sciences of the United States of America | 2008 | 621 |
| 28 | Biomimetic assembly and activation of [FeFe]-hydrogenases | Nature | 2013 | 614 |
| 29 | A library of IR bands of nucleic acids in solution | Biophysical Chemistry | 2003 | 588 |
| 30 | InParanoid 7: new algorithms and tools for eukaryotic orthology analysis | Nucleic Acids Research | 2010 | 581 |
| 31 | A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart | Cell | 2019 | 516 |
| 32 | TOPCONS: consensus prediction of membrane protein topology | Nucleic Acids Research | 2009 | 494 |
| 33 | Structures and Energetics for O2 Formation in Photosystem II | Accounts of Chemical Research | 2009 | 493 |
| 34 | Systematic evaluation of spliced alignment programs for RNA-seq data | Nature Methods | 2013 | 484 |
| 35 | InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic | Nucleic Acids Research | 2015 | 461 |
| 36 | Global Topology Analysis of the Escherichia coli Inner Membrane Proteome | Science | 2005 | 459 |
| 37 | Membrane-protein topology | Nature Reviews Molecular Cell Biology | 2006 | 454 |
| 38 | Improved prediction of protein-protein interactions using AlphaFold2 | Nature Communications | 2022 | 454 |
| 39 | Characterisation of molecular motions in cryo-EM single-particle data by multi-body refinement in RELION | ELife | 2018 | 451 |
| 40 | Central Functions of the Lumenal and Peripheral Thylakoid Proteome of Arabidopsis Determined by Experimentation and Genome-Wide Prediction | Plant Cell | 2002 | 439 |
| 41 | MTH1 inhibition eradicates cancer by preventing sanitation of the dNTP pool | Nature | 2014 | 438 |
| 42 | The antioxidant role of coenzyme Q | Mitochondrion | 2007 | 430 |
| 43 | Shared Molecular Mechanisms of Membrane Transporters | Annual Review of Biochemistry | 2016 | 424 |
| 44 | Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity | Nature Communications | 2018 | 414 |
| 45 | Modulation of the endoplasmic reticulum–mitochondria interface in Alzheimer’s disease and related models | Proceedings of the National Academy of Sciences of the United States of America | 2013 | 395 |
| 46 | Tuning Escherichia coli for membrane protein overexpression | Proceedings of the National Academy of Sciences of the United States of America | 2008 | 392 |
| 47 | Structure is three to ten times more conserved than sequence—A study of structural response in protein cores | Proteins: Structure, Function and Bioinformatics | 2009 | 392 |
| 48 | Influenza A Virus Cell Entry, Replication, Virion Assembly and Movement | Frontiers in Immunology | 2018 | 391 |
| 49 | Spatiotemporal structure of cell fate decisions in murine neural crest | Science | 2019 | 389 |
| 50 | Computational Studies of [NiFe] and [FeFe] Hydrogenases | Chemical Reviews | 2007 | 386 |
