| # | Title | Journal | Year | Citations |
|---|
| 1 | Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein | Cell | 2020 | 6,979 |
| 2 | A robust and high-throughput Cre reporting and characterization system for the whole mouse brain | Nature Neuroscience | 2010 | 5,650 |
| 3 | Crystal Structure of Rhodopsin: A G Protein-Coupled Receptor | Science | 2000 | 5,486 |
| 4 | Quantitative analysis of complex protein mixtures using isotope-coded affinity tags | Nature Biotechnology | 1999 | 4,673 |
| 5 | The preparation and chemical characteristics of hemoglobin-free ghosts of human erythrocytes | Archives of Biochemistry and Biophysics | 1963 | 4,329 |
| 6 | Guidelines for the use and interpretation of assays for monitoring autophagy | Autophagy | 2012 | 3,122 |
| 7 | Accurate prediction of protein structures and interactions using a three-track neural network | Science | 2021 | 2,843 |
| 8 | Direct analysis of protein complexes using mass spectrometry | Nature Biotechnology | 1999 | 2,201 |
| 9 | Interactions between heterologous helix-loop-helix proteins generate complexes that bind specifically to a common DNA sequence | Cell | 1989 | 1,791 |
| 10 | The coagulation cascade: initiation, maintenance, and regulation | Biochemistry | 1991 | 1,736 |
| 11 | Deep Mutational Scanning of SARS-CoV-2 Receptor Binding Domain Reveals Constraints on Folding and ACE2 Binding | Cell | 2020 | 1,726 |
| 12 | Cross-neutralization of SARS-CoV-2 by a human monoclonal SARS-CoV antibody | Nature | 2020 | 1,695 |
| 13 | Protein structure prediction and analysis using the Robetta server | Nucleic Acids Research | 2004 | 1,683 |
| 14 | Rational Design of Envelope Identifies Broadly Neutralizing Human Monoclonal Antibodies to HIV-1 | Science | 2010 | 1,600 |
| 15 | Design of a Novel Globular Protein Fold with Atomic-Level Accuracy | Science | 2003 | 1,471 |
| 16 | Leptin-regulated endocannabinoids are involved in maintaining food intake | Nature | 2001 | 1,468 |
| 17 | Contact order, transition state placement and the refolding rates of single domain proteins 1 1Edited by P. E. Wright | Journal of Molecular Biology | 1998 | 1,449 |
| 18 | Protein Structure Prediction Using Rosetta | Methods in Enzymology | 2004 | 1,445 |
| 19 | Comparing Photosynthetic and Photovoltaic Efficiencies and Recognizing the Potential for Improvement | Science | 2011 | 1,369 |
| 20 | Quantitative reactivity profiling predicts functional cysteines in proteomes | Nature | 2010 | 1,359 |
| 21 | Dramatic growth of mice that develop from eggs microinjected with metallothionein–growth hormone fusion genes | Nature | 1982 | 1,275 |
| 22 | An Adenosine 3′,5′-Monophosphate-dependant Protein Kinase from Rabbit Skeletal Muscle | Journal of Biological Chemistry | 1968 | 1,274 |
| 23 | Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and bayesian scoring functions | Journal of Molecular Biology | 1997 | 1,268 |
| 24 | Mapping Neutralizing and Immunodominant Sites on the SARS-CoV-2 Spike Receptor-Binding Domain by Structure-Guided High-Resolution Serology | Cell | 2020 | 1,195 |
| 25 | Optimal description of a protein structure in terms of multiple groups undergoing TLS motion | Acta Crystallographica Section D: Biological Crystallography | 2006 | 1,175 |
| 26 | Regulation of Yeast Replicative Life Span by TOR and Sch9 in Response to Nutrients | Science | 2005 | 1,171 |
| 27 | Improved protein structure prediction using predicted interresidue orientations | Proceedings of the National Academy of Sciences of the United States of America | 2020 | 1,135 |
| 28 | Kemp elimination catalysts by computational enzyme design | Nature | 2008 | 1,130 |
| 29 | Stable incorporation of plasmid DNA into higher plant cells: the molecular basis of crown gall tumorigenesis | Cell | 1977 | 1,108 |
| 30 | Improving physical realism, stereochemistry, and side‐chain accuracy in homology modeling: Four approaches that performed well in CASP8 | Proteins: Structure, Function and Bioinformatics | 2009 | 1,105 |
| 31 | Requirement for integration of signals from two distinct phosphorylation pathways for activation of MAP kinase | Nature | 1990 | 1,084 |
| 32 | RNA-binding proteins: modular design for efficient function | Nature Reviews Molecular Cell Biology | 2007 | 1,069 |
| 33 | The coming of age of de novo protein design | Nature | 2016 | 1,069 |
| 34 | Predicting protein structures with a multiplayer online game | Nature | 2010 | 1,062 |
| 35 | The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design | Journal of Chemical Theory and Computation | 2017 | 1,032 |
| 36 | De Novo Computational Design of Retro-Aldol Enzymes | Science | 2008 | 1,031 |
| 37 | Protein–Protein Docking with Simultaneous Optimization of Rigid-body Displacement and Side-chain Conformations | Journal of Molecular Biology | 2003 | 1,017 |
| 38 | High-Resolution Comparative Modeling with RosettaCM | Structure | 2013 | 1,010 |
| 39 | Protein tyrosine phosphatases: a diverse family of intracellular and transmembrane enzymes | Science | 1991 | 1,009 |
| 40 | Sensitivity to leptin and susceptibility to seizures of mice lacking neuropeptide Y | Nature | 1996 | 979 |
| 41 | Production of transgenic rabbits, sheep and pigs by microinjection | Nature | 1985 | 975 |
| 42 | NPY/AgRP Neurons Are Essential for Feeding in Adult Mice but Can Be Ablated in Neonates | Science | 2005 | 968 |
| 43 | Waterfall Sequence for Intrinsic Blood Clotting | Science | 1964 | 954 |
| 44 | Multiple Forms of DNA-dependent RNA Polymerase in Eukaryotic Organisms | Nature | 1969 | 918 |
| 45 | Broadly neutralizing antibodies overcome SARS-CoV-2 Omicron antigenic shift | Nature | 2022 | 917 |
| 46 | Matricellular proteins: extracellular modulators of cell function | Current Opinion in Cell Biology | 2002 | 850 |
| 47 | Macromolecular Modeling with Rosetta | Annual Review of Biochemistry | 2008 | 841 |
| 48 | MyoD is a sequence-specific DNA binding protein requiring a region of myc homology to bind to the muscle creatine kinase enhancer | Cell | 1989 | 839 |
| 49 | A Type VI Secretion System of Pseudomonas aeruginosa Targets a Toxin to Bacteria | Cell Host and Microbe | 2010 | 838 |
| 50 | EMRinger: side chain–directed model and map validation for 3D cryo-electron microscopy | Nature Methods | 2015 | 799 |
