Dylan Chivian
TitleCited byYear
Protein structure prediction and analysis using the Robetta server
DE Kim, D Chivian, D Baker
Nucleic acids research 32 (suppl_2), W526-W531, 2004
12052004
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
4052010
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
3872004
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
3622008
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
3362001
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
3192003
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
3012002
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
2342007
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
2262003
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
2052006
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
1772005
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
1722005
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
1242006
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
1202011
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
962005
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, 2018
942018
Genomics for environmental microbiology
AM Deutschbauer, D Chivian, AP Arkin
Current opinion in biotechnology 17 (3), 229-235, 2006
642006
Complete genome sequence of “Enterobacter lignolyticus” SCF1
KM DeAngelis, P D’Haeseleer, D Chivian, JL Fortney, J Khudyakov, ...
Standards in genomic sciences 5 (1), 69, 2011
582011
Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology
L Malmström, M Riffle, CEM Strauss, D Chivian, TN Davis, R Bonneau, ...
PLoS biology 5 (4), 2007
572007
Ab initio methods
D Chivian, T Robertson, R Bonneau, D Baker
Methods of biochemical analysis 44, 547-558, 2003
482003
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Articles 1–20