Protein Structure and Dynamics

Most cited papers

1. A short history of SHELXActa Crystallographica Section A Foundations of Crystallography · 2007 · 87,967 citations
2. UCSF Chimera—A visualization system for exploratory research and analysisJournal of Computational Chemistry · 2004 · 48,921 citations
3. Highly accurate protein structure prediction with AlphaFoldNature · 2021 · 47,923 citations
4. AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreadingJournal of Computational Chemistry · 2009 · 38,969 citations
5. Features and development of CootActa Crystallographica Section D Biological Crystallography · 2010 · 30,465 citations
6. PHENIX : a comprehensive Python-based system for macromolecular structure solutionActa Crystallographica Section D Biological Crystallography · 2010 · 24,964 citations
7. PROCHECK: a program to check the stereochemical quality of protein structuresJournal of Applied Crystallography · 1993 · 24,851 citations
8. Canonical dynamics: Equilibrium phase-space distributionsPhysical Review A · 1985 · 23,997 citations
9. A smooth particle mesh Ewald methodThe Journal of Chemical Physics · 1995 · 23,457 citations
10. Isolation of biologically active ribonucleic acid from sources enriched in ribonucleaseBiochemistry · 1979 · 22,200 citations
11. Phaser crystallographic softwareJournal of Applied Crystallography · 2007 · 21,424 citations
12. Polymorphic transitions in single crystals: A new molecular dynamics methodJournal of Applied Physics · 1981 · 20,838 citations
13. The Reliability of Molecular Weight Determinations by Dodecyl Sulfate-Polyacrylamide Gel ElectrophoresisJournal of Biological Chemistry · 1969 · 20,327 citations
14. Development and testing of a general amber force fieldJournal of Computational Chemistry · 2004 · 20,311 citations
15. GROMACS: Fast, flexible, and freeJournal of Computational Chemistry · 2005 · 19,704 citations
16. Canonical sampling through velocity rescalingThe Journal of Chemical Physics · 2007 · 19,121 citations
17. Minimap2: pairwise alignment for nucleotide sequencesBioinformatics · 2018 · 17,805 citations
18. Scalable molecular dynamics with NAMDJournal of Computational Chemistry · 2005 · 17,570 citations
19. LINCS: A linear constraint solver for molecular simulationsJournal of Computational Chemistry · 1997 · 17,549 citations
20. GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular SimulationJournal of Chemical Theory and Computation · 2008 · 16,231 citations
21. Accurate structure prediction of biomolecular interactions with AlphaFold 3Nature · 2024 · 16,230 citations
22. Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical featuresBiopolymers · 1983 · 15,912 citations
23. Crystallography & NMR System: A New Software Suite for Macromolecular Structure DeterminationActa Crystallographica Section D Biological Crystallography · 1998 · 15,802 citations
24. CHARMM : A program for macromolecular energy, minimization, and dynamics calculationsJournal of Computational Chemistry · 1983 · 15,033 citations
25. MolProbity : all-atom structure validation for macromolecular crystallographyActa Crystallographica Section D Biological Crystallography · 2009 · 14,920 citations
26. All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of ProteinsThe Journal of Physical Chemistry B · 1998 · 14,683 citations
27. The Pfam Protein Families DatabaseNucleic Acids Research · 2002 · 14,196 citations
28. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structuresJournal of Applied Crystallography · 1991 · 14,157 citations
29. SWISS-MODEL: homology modelling of protein structures and complexesNucleic Acids Research · 2018 · 14,106 citations
30. Overview of the CCP 4 suite and current developmentsActa Crystallographica Section D Biological Crystallography · 2011 · 12,716 citations
31. Squeeze-and-Excitation NetworksIEEE Transactions on Pattern Analysis and Machine Intelligence · 2019 · 12,714 citations
32. Improved methods for building protein models in electron density maps and the location of errors in these modelsActa Crystallographica Section A Foundations of Crystallography · 1991 · 12,688 citations
33. ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SBJournal of Chemical Theory and Computation · 2015 · 11,600 citations
34. SWISS‐MODEL and the Swiss‐Pdb Viewer: An environment for comparative protein modelingElectrophoresis · 1997 · 11,382 citations
35. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy functionJournal of Computational Chemistry · 1998 · 10,968 citations
36. Avogadro: an advanced semantic chemical editor, visualization, and analysis platformJournal of Cheminformatics · 2012 · 10,819 citations
37. ColabFold: making protein folding accessible to allNature Methods · 2022 · 10,204 citations
38. Glide: A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking AccuracyJournal of Medicinal Chemistry · 2004 · 10,203 citations
39. The Amber biomolecular simulation programsJournal of Computational Chemistry · 2005 · 9,808 citations
40. Extended-Connectivity FingerprintsJournal of Chemical Information and Modeling · 2010 · 8,040 citations
41. GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkitBioinformatics · 2013 · 7,748 citations
42. AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python BindingsJournal of Chemical Information and Modeling · 2021 · 7,558 citations
43. Extra Precision Glide: Docking and Scoring Incorporating a Model of Hydrophobic Enclosure for Protein−Ligand ComplexesJournal of Medicinal Chemistry · 2006 · 7,040 citations
44. LigPlot+: Multiple Ligand–Protein Interaction Diagrams for Drug DiscoveryJournal of Chemical Information and Modeling · 2011 · 6,739 citations
45. Drug Combination Studies and Their Synergy Quantification Using the Chou-Talalay MethodCancer Research · 2010 · 5,875 citations
46. The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinitiesExpert Opinion on Drug Discovery · 2015 · 5,668 citations
47. Thermodynamics of protein association reactions: forces contributing to stabilityBiochemistry · 1981 · 5,576 citations
48. PRODRG: a tool for high-throughput crystallography of protein–ligand complexesActa Crystallographica Section D Biological Crystallography · 2004 · 4,855 citations
49. SwissTargetPrediction: updated data and new features for efficient prediction of protein targets of small moleculesNucleic Acids Research · 2019 · 4,628 citations
50. PHENIX : building new software for automated crystallographic structure determinationActa Crystallographica Section D Biological Crystallography · 2002 · 4,427 citations