| # | Title | Journal | Year | Citations |
|---|
| 1 | THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method | Journal of Computational Chemistry | 1992 | 5,736 |
| 2 | Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition) | Autophagy | 2016 | 4,701 |
| 3 | UCSF ChimeraX: Structure visualization for researchers, educators, and developers | Protein Science | 2021 | 4,478 |
| 4 | A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations | Journal of Computational Chemistry | 2003 | 4,028 |
| 5 | How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? | Journal of Computational Chemistry | 2000 | 3,725 |
| 6 | UCSF ChimeraX: Meeting modern challenges in visualization and analysis | Protein Science | 2018 | 3,377 |
| 7 | ZINC − A Free Database of Commercially Available Compounds for Virtual Screening | Journal of Chemical Information and Modeling | 2005 | 3,366 |
| 8 | ProteomeXchange provides globally coordinated proteomics data submission and dissemination | Nature Biotechnology | 2014 | 2,505 |
| 9 | From Levinthal to pathways to funnels | Nature Structural and Molecular Biology | 1997 | 2,125 |
| 10 | Statistical potential for assessment and prediction of protein structures | Protein Science | 2006 | 2,104 |
| 11 | ZINC: A Free Tool to Discover Chemistry for Biology | Journal of Chemical Information and Modeling | 2012 | 1,985 |
| 12 | Reaching for high-hanging fruit in drug discovery at protein–protein interfaces | Nature | 2007 | 1,777 |
| 13 | Relating protein pharmacology by ligand chemistry | Nature Biotechnology | 2007 | 1,722 |
| 14 | Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking | Journal of Medicinal Chemistry | 2012 | 1,574 |
| 15 | Automated design of synthetic ribosome binding sites to control protein expression | Nature Biotechnology | 2009 | 1,560 |
| 16 | Interaction of Nitric Oxide Synthase with the Postsynaptic Density Protein PSD-95 and α1-Syntrophin Mediated by PDZ Domains | Cell | 1996 | 1,557 |
| 17 | Predicting new molecular targets for known drugs | Nature | 2009 | 1,474 |
| 18 | Principles of protein folding — A perspective from simple exact models | Protein Science | 1995 | 1,321 |
| 19 | ZINC--a free database of commercially available compounds for virtual screening | Protein Science | 2005 | 1,225 |
| 20 | Benchmarking Sets for Molecular Docking | Journal of Medicinal Chemistry | 2006 | 1,184 |
| 21 | AMBER: Assisted model building with energy refinement. A general program for modeling molecules and their interactions | Journal of Computational Chemistry | 1981 | 1,104 |
| 22 | Role of Accurate Mass Measurement (±10 ppm) in Protein Identification Strategies Employing MS or MS/MS and Database Searching | Analytical Chemistry | 1999 | 1,096 |
| 23 | The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design | Journal of Chemical Theory and Computation | 2017 | 1,032 |
| 24 | DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases | Journal of Computer-Aided Molecular Design | 2001 | 1,022 |
| 25 | Small-Molecule Inhibitors of Protein-Protein Interactions: Progressing toward the Reality | Chemistry and Biology | 2014 | 865 |
| 26 | (null) | Journal of Computer - Aided Molecular Design | 2000 | 805 |
| 27 | Visualizing density maps with UCSF Chimera | Journal of Structural Biology | 2007 | 802 |
| 28 | Structural basis of substrate specificity in the serine proteases | Protein Science | 1995 | 726 |
| 29 | The Catalytic Mechanism and Structure of Thymidylate Synthase | Annual Review of Biochemistry | 1995 | 707 |
| 30 | Ultra-large library docking for discovering new chemotypes | Nature | 2019 | 595 |
| 31 | DOCK 6: Impact of new features and current docking performance | Journal of Computational Chemistry | 2015 | 552 |
| 32 | Widespread Protein Aggregation as an Inherent Part of Aging in C. elegans | PLoS Biology | 2010 | 551 |
| 33 | clusterMaker: a multi-algorithm clustering plugin for Cytoscape | BMC Bioinformatics | 2011 | 541 |
| 34 | Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: a new homology modeling tool | Journal of Molecular Biology | 1997 | 529 |
| 35 | Structure of the µ-opioid receptor–Gi protein complex | Nature | 2018 | 527 |
| 36 | Comparison of diffusion- and T2-weighted MRI for the early detection of cerebral ischemia and reperfusion in rats | Magnetic Resonance in Medicine | 1991 | 514 |
| 37 | ModBase, a database of annotated comparative protein structure models, and associated resources | Nucleic Acids Research | 2011 | 506 |
| 38 | Binding of Small-Molecule Ligands to Proteins: “What You See” Is Not Always “What You Get” | Structure | 2009 | 500 |
| 39 | Biomolecular Simulations: Recent Developments in Force Fields, Simulations of Enzyme Catalysis, Protein-Ligand, Protein-Protein, and Protein-Nucleic Acid Noncovalent Interactions | Annual Review of Biophysics and Biomolecular Structure | 2001 | 495 |
| 40 | Accurate SAXS Profile Computation and its Assessment by Contrast Variation Experiments | Biophysical Journal | 2013 | 489 |
| 41 | Binding of a Diverse Set of Ligands to Avidin and Streptavidin: An Accurate Quantitative Prediction of Their Relative Affinities by a Combination of Molecular Mechanics and Continuum Solvent Models | Journal of Medicinal Chemistry | 2000 | 483 |
| 42 | Faster STORM using compressed sensing | Nature Methods | 2012 | 473 |
| 43 | Chemical Approaches to Triggerable Lipid Vesicles for Drug and Gene Delivery | Accounts of Chemical Research | 2003 | 449 |
| 44 | A Synthetic Genetic Edge Detection Program | Cell | 2009 | 442 |
| 45 | MULTI-seq: sample multiplexing for single-cell RNA sequencing using lipid-tagged indices | Nature Methods | 2019 | 421 |
| 46 | Cyclic ADP-ribose production by CD38 regulates intracellular calcium release, extracellular calcium influx and chemotaxis in neutrophils and is required for bacterial clearance in vivo | Nature Medicine | 2001 | 413 |
| 47 | Protein folding in the landscape perspective: Chevron plots and non-arrhenius kinetics | Nature Medicine | 1998 | 397 |
| 48 | A detergent-based assay for the detection of promiscuous inhibitors | Nature Protocols | 2006 | 397 |
| 49 | Molecular docking using shape descriptors | Journal of Computational Chemistry | 1992 | 393 |
| 50 | Atmospheric Pressure Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry | Analytical Chemistry | 2000 | 391 |
