| # | Title | Journal | Year | Citations |
|---|
| 1 | Creating the CIPRES Science Gateway for inference of large phylogenetic trees | Gastroenterology | 2010 | 6,701 |
| 2 | Clustering of highly homologous sequences to reduce the size of large protein databases | Bioinformatics | 2001 | 895 |
| 3 | Comparison of sequence profiles. Strategies for structural predictions using sequence information | Protein Science | 2000 | 431 |
| 4 | Regulatory subunit of protein kinase A: structure of deletion mutant with cAMP binding domains | Science | 1995 | 378 |
| 5 | Adaptive computing on the grid using AppLeS | IEEE Transactions on Parallel and Distributed Systems | 2003 | 348 |
| 6 | The Molecular Biology Toolkit (MBT): a modular platform for developing molecular visualization applications | BMC Bioinformatics | 2005 | 257 |
| 7 | The GPCR Network: a large-scale collaboration to determine human GPCR structure and function | Nature Reviews Drug Discovery | 2013 | 252 |
| 8 | Emergent semantics through interaction in image databases | IEEE Transactions on Knowledge and Data Engineering | 2001 | 153 |
| 9 | [30] Macromolecular crystallographic information file | Methods in Enzymology | 1997 | 148 |
| 10 | Integrative analysis of multimodal mass spectrometry data in MZmine 3 | Nature Biotechnology | 2023 | 124 |
| 11 | CAFASP-1: Critical assessment of fully automated structure prediction methods | Nature Biotechnology | 1999 | 110 |
| 12 | PEBIL: Efficient static binary instrumentation for Linux | Nature Biotechnology | 2010 | 105 |
| 13 | Paramfit: Automated optimization of force field parameters for molecular dynamics simulations | Journal of Computational Chemistry | 2015 | 91 |
| 14 | [13] Identification of sequence patterns with profile analysis | Methods in Enzymology | 1996 | 90 |
| 15 | Expected seismic shaking in Los Angeles reduced by San Andreas fault zone plasticity | Geophysical Research Letters | 2014 | 79 |
| 16 | Saturated BLAST: an automated multiple intermediate sequence search used to detect distant homology | Bioinformatics | 2000 | 69 |
| 17 | Web-Based Telemicroscopy | Journal of Structural Biology | 1999 | 60 |
| 18 | CAFASP-1: critical assessment of fully automated structure prediction methods | Proteins: Structure, Function and Bioinformatics | 1999 | 60 |
| 19 | Computational simulations of the Trichoderma reesei cellobiohydrolase I acting on microcrystalline cellulose Iβ: the enzyme–substrate complex | Carbohydrate Research | 2009 | 49 |
| 20 | Quantum Mechanical Designs toward Planar Delocalized Cyclooctatetraene: A New Target for Synthesis | Journal of the American Chemical Society | 2001 | 48 |
| 21 | Interactions of the complete cellobiohydrolase I from Trichodera reesei with microcrystalline cellulose Iβ | Cellulose | 2008 | 46 |
| 22 | A genetic algorithms approach to modeling the performance of memory-bound computations | Cellulose | 2007 | 45 |
| 23 | BioJava 5: A community driven open-source bioinformatics library | PLoS Computational Biology | 2019 | 44 |
| 24 | Progress in modelling fast-ion D-alpha spectra and neutral particle analyzer fluxes using FIDASIM | Plasma Physics and Controlled Fusion | 2020 | 43 |
| 25 | Molecular modeling of solvation. Cl−(D2O) | Journal of Chemical Physics | 1991 | 42 |
| 26 | Analysis of inflammatory and lipid metabolic networks across RAW264.7 and thioglycolate-elicited macrophages | Journal of Lipid Research | 2013 | 41 |
| 27 | Nimrod/K: Towards massively parallel dynamic Grid workflows | Journal of Lipid Research | 2008 | 40 |
| 28 | Hidden Markov Model Analysis of Motifs in Steroid Dehydrogenases and Their Homologs | Biochemical and Biophysical Research Communications | 1997 | 38 |
| 29 | Reduced-order modelling of biochemical networks: application to the GTPase-cycle signalling module | IET Systems Biology | 2005 | 38 |
| 30 | Opal: SimpleWeb Services Wrappers for Scientific Applications | IET Systems Biology | 2006 | 33 |
| 31 | Reaction path power series analysis of NH3 inversion | Journal of Chemical Physics | 1990 | 31 |
| 32 | Controlled publication of digital scientific data | Communications of the ACM | 2002 | 31 |
| 33 | Modeling and predicting performance of high performance computing applications on hardware accelerators | International Journal of High Performance Computing Applications | 2013 | 30 |
| 34 | A scalable and accurate method for classifying protein–ligand binding geometries using a MapReduce approach | Computers in Biology and Medicine | 2012 | 27 |
| 35 | Directing Power of Cyclobutenoid Annelations on the Double Bonds of Planar Cyclooctatetraenes | Journal of the American Chemical Society | 2002 | 22 |
| 36 | The Virtual Instrument: Support for Grid-Enabled Mcell Simulations | International Journal of High Performance Computing Applications | 2004 | 22 |
| 37 | An analysis of the Protein Data Bank in search of temporal and global trends | Bioinformatics | 1999 | 21 |
| 38 | Exploring the Performance Benefit of Hybrid Memory System on HPC Environments | Bioinformatics | 2017 | 21 |
| 39 | Enabling fair pricing on HPC systems with node sharing | Bioinformatics | 2013 | 20 |
| 40 | Quantification of Fault-Zone Plasticity Effects with Spontaneous Rupture Simulations | Pure and Applied Geophysics | 2017 | 20 |
| 41 | Evidence of Exponential Speed-Up in the Solution of Hard Optimization Problems | Complexity | 2018 | 20 |
| 42 | Characterizing the Performance-Energy Tradeoff of Small ARM Cores in HPC Computation | Lecture Notes in Computer Science | 2014 | 19 |
| 43 | An end-to-end Web services-based infrastructure for biomedical applications | Lecture Notes in Computer Science | 2005 | 18 |
| 44 | Knowledge-based Grids | Mass Storage Systems and Technologies(MSS), Proceedings of the NASA Goddard Conference on | 2001 | 17 |
| 45 | Crystal structure of a putative PII-like signaling protein (TM0021) from Thermotoga maritima at 2.5 Å resolution | Proteins: Structure, Function and Bioinformatics | 2004 | 17 |
| 46 | Crystal structure of a putative oxalate decarboxylase (TM1287) from Thermotoga maritima at 1.95 Å resolution | Proteins: Structure, Function and Bioinformatics | 2004 | 16 |
| 47 | Crystal structure of S-adenosylmethionine:tRNA ribosyltransferase-isomerase (QueA) from Thermotoga maritima at 2.0 Å resolution reveals a new fold | Proteins: Structure, Function and Bioinformatics | 2005 | 16 |
| 48 | Modeling and predicting application performance on parallel computers using HPC challenge benchmarks | Parallel and Distributed Processing Symposium (IPDPS), Proceedings of the International Conference on | 2008 | 16 |
| 49 | The Cotton–Mouton effect of gaseous CO2, N2O, OCS, and CS2. A cubic response multiconfigurational self-consistent field study | Journal of Chemical Physics | 2001 | 15 |
| 50 | Crystal structure of a single-stranded DNA-binding protein (TM0604) from Thermotoga maritima at 2.60 Å resolution | Proteins: Structure, Function and Bioinformatics | 2006 | 15 |
