• 463 Citations
  • 11 h-Index
20082019
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Research Output 2008 2019

  • 463 Citations
  • 11 h-Index
  • 13 Article
  • 4 Review article
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Article
2019

ECOD: Identification of distant homology among multidomain and transmembrane domain proteins

Schaeffer, R. D., Kinch, L., Medvedev, K. E., Pei, J., Cheng, H. & Grishin, N. V., Jun 21 2019, In : BMC Molecular and Cell Biology. 20, 1, 18.

Research output: Contribution to journalArticle

Open Access
Leucine-tRNA Ligase
ATP-Binding Cassette Transporters
Dimerization
Anniversaries and Special Events
Leucine
2018
1 Citation (Scopus)

A sequence family database built on ECOD structural domains

Liao, Y., Schaeffer, R. D., Pei, J. & Grishin, N. V., Sep 1 2018, In : Bioinformatics. 34, 17, p. 2997-3003 7 p.

Research output: Contribution to journalArticle

Databases
Alignment
Selection Bias
Sequence Alignment
Seeds
2 Citations (Scopus)

Searching ECOD for Homologous Domains by Sequence and Structure

Schaeffer, R. D., Liao, Y. & Grishin, N. V., Mar 1 2018, In : Current Protocols in Bioinformatics. 61, 1, e45.

Research output: Contribution to journalArticle

Sequence Homology
Proteins
Databases
Functional analysis
Information Storage and Retrieval
2017
17 Citations (Scopus)

ECOD: New developments in the evolutionary classification of domains

Dustin Schaeffer, R., Liao, Y., Cheng, H. & Grishin, N. V., Jan 1 2017, In : Nucleic Acids Research. 45, D1, p. D296-D302

Research output: Contribution to journalArticle

Databases
Proteins
Protein Domains
Direction compound
2016
19 Citations (Scopus)

CASP 11 target classification

Kinch, L. N., Li, W., Schaeffer, R. D., Dunbrack, R. L., Monastyrskyy, B., Kryshtafovych, A. & Grishin, N. V., Sep 1 2016, In : Proteins. 84, p. 20-33 14 p.

Research output: Contribution to journalArticle

Servers
Protein Databases
Proteins
Deterioration
Experiments
4 Citations (Scopus)

Estimation of Uncertainties in the Global Distance Test (GDT_TS) for CASP Models

Li, W., Schaeffer, R. D., Otwinowski, Z. & Grishin, N. V., 2016, In : PLoS One. 11, 5, p. e0154786

Research output: Contribution to journalArticle

Uncertainty
uncertainty
X-Rays
X-radiation
X rays
2015
14 Citations (Scopus)

Manual classification strategies in the ECOD database

Cheng, H., Liao, Y., Schaeffer, R. D. & Grishin, N. V., Jul 1 2015, In : Proteins: Structure, Function and Bioinformatics. 83, 7, p. 1238-1251 14 p.

Research output: Contribution to journalArticle

Protein Databases
Proteins
Databases
Protein Domains
Computational Biology
2014
92 Citations (Scopus)

ECOD: An Evolutionary Classification of Protein Domains

Cheng, H., Schaeffer, R. D., Liao, Y., Kinch, L. N., Pei, J., Shi, S., Kim, B. H. & Grishin, N. V., Dec 1 2014, In : PLoS Computational Biology. 10, 12

Research output: Contribution to journalArticle

Proteins
Protein
protein
proteins
Protein Structure
2011
25 Citations (Scopus)

Generation of a consensus protein domain dictionary

Schaeffer, R. D., Jonsson, A. L., Simms, A. M. & Daggett, V., Jan 1 2011, In : Bioinformatics. 27, 1, p. 46-54 9 p., btq625.

Research output: Contribution to journalArticle

Glossaries
Proteins
Protein
Fold
Folding
16 Citations (Scopus)

Malleability of folding intermediates in the homeodomain superfamily

Banachewicz, W., Religa, T. L., Schaeffer, R. D., Daggett, V. & Fersht, A. R., Apr 5 2011, In : Proceedings of the National Academy of Sciences of the United States of America. 108, 14, p. 5596-5601 6 p.

Research output: Contribution to journalArticle

Helix-Turn-Helix Motifs
Molecular Dynamics Simulation
Peptides
12 Citations (Scopus)

Manifestations of native topology in the denatured state ensemble of rhodopseudomonas palustris cytochrome c′

Dar, T. A., Schaeffer, R. D., Daggett, V. & Bowler, B. E., Feb 15 2011, In : Biochemistry. 50, 6, p. 1029-1041 13 p.

Research output: Contribution to journalArticle

Rhodopseudomonas
Cytochromes c
Heme
Histidine
Guanidine
2010
93 Citations (Scopus)

Dynameomics: A Comprehensive Database of Protein Dynamics

van der Kamp, M. W., Schaeffer, R. D., Jonsson, A. L., Scouras, A. D., Simms, A. M., Toofanny, R. D., Benson, N. C., Anderson, P. C., Merkley, E. D., Rysavy, S., Bromley, D., Beck, D. A. C. & Daggett, V., Mar 1 2010, In : Structure. 18, 4, p. 423-435 13 p.

Research output: Contribution to journalArticle

Protein Databases
Protein Folding
Databases
Proteins
Protein Unfolding
2008
52 Citations (Scopus)

Dynameomics: Mass annotation of protein dynamics and unfolding in water by high-throughput atomistic molecular dynamics simulations

Beck, D. A. C., Jonsson, A. L., Schaeffer, R. D., Scott, K. A., Day, R., Toofanny, R. D., Alonso, D. O. V. & Daggett, V., Jun 1 2008, In : Protein Engineering, Design and Selection. 21, 6, p. 353-368 16 p.

Research output: Contribution to journalArticle

Protein Unfolding
Molecular Dynamics Simulation
Molecular dynamics
Throughput
Proteins