Protein structure prediction and analysis using the Robetta server DE Kim, D Chivian, D Baker Nucleic acids research 32 (suppl_2), W526-W531, 2004 | 2165 | 2004 |
KBase: the United States department of energy systems biology knowledgebase AP Arkin, RW Cottingham, CS Henry, NL Harris, RL Stevens, S Maslov, ... Nature biotechnology 36 (7), 566-569, 2018 | 1078 | 2018 |
A genomic catalog of Earth’s microbiomes S Nayfach, S Roux, R Seshadri, D Udwary, N Varghese, F Schulz, D Wu, ... Nature biotechnology 39 (4), 499-509, 2021 | 586 | 2021 |
MicrobesOnline: an integrated portal for comparative and functional genomics PS Dehal, MP Joachimiak, MN Price, JT Bates, JK Baumohl, D Chivian, ... Nucleic acids research 38 (suppl_1), D396-D400, 2010 | 532 | 2010 |
Environmental genomics reveals a single-species ecosystem deep within Earth D Chivian, EL Brodie, EJ Alm, DE Culley, PS Dehal, TZ DeSantis, ... Science 322 (5899), 275-278, 2008 | 529 | 2008 |
Modeling structurally variable regions in homologous proteins with rosetta CA Rohl, CEM Strauss, D Chivian, D Baker Proteins: Structure, Function, and Bioinformatics 55 (3), 656-677, 2004 | 424 | 2004 |
Rosetta in CASP4: progress in ab initio protein structure prediction R Bonneau, J Tsai, I Ruczinski, D Chivian, C Rohl, CEM Strauss, D Baker Proteins: Structure, Function, and Bioinformatics 45 (S5), 119-126, 2001 | 409 | 2001 |
Automated prediction of CASP‐5 structures using the Robetta server D Chivian, DE Kim, L Malmström, P Bradley, T Robertson, P Murphy, ... Proteins: Structure, Function, and Bioinformatics 53 (S6), 524-533, 2003 | 371 | 2003 |
De novo prediction of three-dimensional structures for major protein families R Bonneau, CEM Strauss, CA Rohl, D Chivian, P Bradley, L Malmström, ... Journal of molecular biology 322 (1), 65-78, 2002 | 330 | 2002 |
Structure prediction for CASP7 targets using extensive all‐atom refinement with Rosetta@ home R Das, B Qian, S Raman, R Vernon, J Thompson, P Bradley, S Khare, ... Proteins: Structure, Function, and Bioinformatics 69 (S8), 118-128, 2007 | 274 | 2007 |
Rosetta predictions in CASP5: successes, failures, and prospects for complete automation P Bradley, D Chivian, J Meiler, KMS Misura, CA Rohl, WR Schief, ... Proteins: Structure, Function, and Bioinformatics 53 (S6), 457-468, 2003 | 248 | 2003 |
Physically realistic homology models built with rosetta can be more accurate than their templates KMS Misura, D Chivian, CA Rohl, DE Kim, D Baker Proceedings of the National Academy of Sciences 103 (14), 5361-5366, 2006 | 227 | 2006 |
Free modeling with Rosetta in CASP6 P Bradley, L Malmström, B Qian, J Schonbrun, D Chivian, DE Kim, ... Proteins: Structure, Function, and Bioinformatics 61 (S7), 128-134, 2005 | 201 | 2005 |
Prediction of CASP6 structures using automated Robetta protocols D Chivian, DE Kim, L Malmström, J Schonbrun, CA Rohl, D Baker Proteins: Structure, Function, and Bioinformatics 61 (S7), 157-166, 2005 | 197 | 2005 |
Optimization of a heterologous mevalonate pathway through the use of variant HMG-CoA reductases SM Ma, DE Garcia, AM Redding-Johanson, GD Friedland, R Chan, ... Metabolic engineering 13 (5), 588-597, 2011 | 182 | 2011 |
Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection D Chivian, D Baker Nucleic acids research 34 (17), e112-e112, 2006 | 145 | 2006 |
Automated prediction of domain boundaries in CASP6 targets using Ginzu and RosettaDOM DE Kim, D Chivian, L Malmström, D Baker Proteins: Structure, Function, and Bioinformatics 61 (S7), 193-200, 2005 | 114 | 2005 |
Complete genome sequence of “Enterobacter lignolyticus” SCF1 KM DeAngelis, P D’Haeseleer, D Chivian, JL Fortney, J Khudyakov, ... Standards in genomic sciences 5, 69-85, 2011 | 87 | 2011 |
The DOE systems biology knowledgebase (KBase) AP Arkin, RL Stevens, RW Cottingham, S Maslov, CS Henry, P Dehal, ... BioRxiv, 096354, 2016 | 79 | 2016 |
Single cell genomics indicates horizontal gene transfer and viral infections in a deep subsurface Firmicutes population JM Labonté, EK Field, M Lau, D Chivian, E Van Heerden, KE Wommack, ... Frontiers in microbiology 6, 137143, 2015 | 75 | 2015 |