The DOI matches its Crossref record; 65 of the 65 references it cites were found in a registry or an index.
Progress in Modeling of Protein Structures and Interactions.
Abstract
The prediction of the structures and interactions of biological macromolecules at the atomic level and the design of new structures and interactions are critical tests of our understanding of the interatomic interactions that underlie molecular biology. Equally important, the capability to accurately predict and design macromolecular structures and interactions would streamline the interpretation of genome sequence information and allow the creation of macromolecules with new and useful functions. This review summarizes recent progress in modeling that suggests that we are entering an era in which high-resolution prediction and design will make increasingly important contributions to biology and medicine.
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In the citing paper
“Only recently it has been realized that proteins are not random heteropolymers but their sequences are formed following a tentative design (for a review see [39], [40]).”
From Lethal mutants and truncated selection together solve a paradox of the origin of life (2011) · cites this paper as [40]
Citations
Cites
1 retracted
Computational Design of a Biologically Active Enzyme
Dwyer, M. A., Looger, L. L., & Hellinga, H. W. (2004) · Science · doi:10.1126/science.1098432 · Cited by 295
RetractedGapped BLAST and PSI-BLAST: a new generation of protein database search programs
Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
Brooks, B., Bruccoleri, R., Olafson, B. D., States, D., Swaminathan, S., & Karplus, M. (1983) · Journal of Computational Chemistry · doi:10.1002/jcc.540040211 · Cited by 13,736
A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules
Cornell, W. D., Cieplak, P., Bayly, C. I., Gould, I. R., Merz, K. M., Ferguson, D. M., Spellmeyer, D. C., Fox, T., Caldwell, J. W., & Kollman, P. A. (1995) · Journal of the American Chemical Society · doi:10.1021/ja00124a002 · Cited by 13,111
Principles that Govern the Folding of Protein Chains
Anfinsen, C. B. (1973) · Science · doi:10.1126/science.181.4096.223 · Cited by 7,096
Jones, D. T. (1999) · Journal of Molecular Biology · doi:10.1006/jmbi.1999.3091 · Cited by 5,522
Molecular dynamics simulations of biomolecules
Karplus, M., & McCammon, J. (2002) · Nature Structural Biology · doi:10.1038/nsb0902-646 · Cited by 3,401
HADDOCK: A Protein−Protein Docking Approach Based on Biochemical or Biophysical Information
Dominguez, C., Boelens, R., & Bonvin, A. M. J. J. (2003) · Journal of the American Chemical Society · doi:10.1021/ja026939x · Cited by 3,187
Funnels, pathways, and the energy landscape of protein folding: A synthesis
Bryngelson, J. D., Onuchic, J. N., Socci, N. D., & Wolynes, P. G. (1995) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.340210302 · Cited by 2,648
A hierarchical approach to all‐atom protein loop prediction
Jacobson, M. P., Pincus, D. L., Rapp, C. S., Day, T., Honig, B. H., Shaw, D. E., & Friesner, R. A. (2004) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.10613 · Cited by 2,541
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Cited by
Sorted by citations
Macromolecular Modeling with Rosetta
Das, R., & Baker, D. A. (2008) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.77.062906.171838 · Cited by 995
Self-citationPrinciples of Protein−Protein Interactions: What are the Preferred Ways For Proteins To Interact?
Keskin, O., Gursoy, A., Ma, B., & Nussinov, R. (2008) · Chemical Reviews · doi:10.1021/cr040409x · Cited by 697
Protein structure determination from NMR chemical shifts
Cavalli, A., Salvatella, X., Dobson, C. M., & Vendruscolo, M. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0610313104 · Cited by 557
Modeling electrostatic effects in proteins
Warshel, A., Sharma, P. K., Kato, M., & Parson, W. W. (2006) · Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics · doi:10.1016/j.bbapap.2006.08.007 · Cited by 526
Konrad, M., Schaller, A., Seelow, D., Pandey, A. V., Waldegger, S., Lesslauer, A., Vitzthum, H., Suzuki, Y., Luk, J. M., Becker, C., et al. (2006) · The American Journal of Human Genetics · doi:10.1086/508617 · Cited by 525
“A 3D model of the first 115 aa of claudin-19 was constructed using ROSETTA de novo methods, with use of a structure library of protein fragments.(14) Quality of the model was checked by WHATCHECK(15) and Ramachandran plot analysis.”
Method
Metadata
- Authors
- Schueler-Furman, O., Wang, C., Bradley, P., Misura, K., & Baker, D.
- Affiliations
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
- Howard Hughes Medical Institute (US)
- Corresponding author
- Baker, David
- Venue
- Science
- Published
- 2005-10-28
- Volume
- 310
- Issue
- 5748
- Pages
- 638-642
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- OpenAlex
- W2147752484
- Cited by
- 294
- References
- 65
- Citations by year
- 2025: 4 · 2024: 4 · 2023: 2 · 2022: 2 · 2021: 4 · 2020: 5 · 2019: 8 · 2018: 2 · 2017: 8 · 2016: 9 · 2015: 9 · 2014: 8 · 2013: 10 · 2012: 16
- FWCI
- 3.31
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
- Life Sciences › Pharmacology, Toxicology and Pharmaceutics › Drug Discovery › Computational Drug Discovery Methods
- Keywords
- protein structure prediction, protein-protein interaction, interatomic interactions, genome interpretation
- MeSH terms
- Computer Simulation, Computing Methodologies, Models, Molecular, Protein Conformation
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