| 1. |
- Branden, CI, et al.
(författare)
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Proteins
- 1997
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Ingår i: Current opinion in structural biology. - 0959-440X. ; 7:6, s. 819-820
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 2. |
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| 3. |
- Lindqvist, Y, et al.
(författare)
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Protein-biotin interactions
- 1996
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Ingår i: Current opinion in structural biology. - 0959-440X. ; 6:6, s. 798-803
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Tidskriftsartikel (refereegranskat)
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| 4. |
- Aqvist, Johan, et al.
(författare)
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Bridging the gap between ribosome structure and biochemistry by mechanistic computations
- 2012
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Ingår i: Current opinion in structural biology. - : Elsevier BV. - 0959-440X .- 1879-033X. ; 22:6, s. 815-823
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Tidskriftsartikel (refereegranskat)abstract
- The wealth of structural and biochemical data now available for protein synthesis on the ribosome presents major new challenges for computational biochemistry. Apart from technical difficulties in modeling ribosome systems, the complexity of the overall translation cycle with a multitude of different kinetic steps presents a formidable problem for computational efforts where we have only seen the beginning. However, a range of methodologies including molecular dynamics simulations, free energy calculations, molecular docking and quantum chemical approaches have already been put to work with promising results. In particular, the combined efforts of structural biology, biochemistry, kinetics and computational modeling can lead towards a quantitative structure-based description of translation.
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| 5. |
- Azinas, Stavros, et al.
(författare)
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Cryo-EM uniqueness in structure determination of macromolecular complexes : A selected structural anthology
- 2023
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Ingår i: Current opinion in structural biology. - 0959-440X .- 1879-033X. ; 81
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Tidskriftsartikel (refereegranskat)abstract
- Cryogenic electron microscopy (cryo-EM) has become in the past 10 years one of the major tools for the structure determination of proteins. Nowadays, the structure prediction field is experiencing the same revolution and, using AlphaFold2, it is possible to have high-confidence atomic models for virtually any polypeptide chain, smaller than 4000 amino acids, in a simple click. Even in a scenario where all polypeptide chain folding were to be known, cryo-EM retains specific characteristics that make it a unique tool for the structure determination of macromolecular complexes. Using cryo-EM, it is possible to obtain near-atomic structures of large and flexible megacomplexes, describe conformational panoramas, and potentially develop a structural proteomic approach from fully ex vivo specimens.
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| 6. |
- Bacic, Luka, et al.
(författare)
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Recent advances in single-molecule fluorescence microscopy render structural biology dynamic
- 2020
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Ingår i: Current opinion in structural biology. - LONDON ENGLAND : Elsevier BV. - 0959-440X .- 1879-033X. ; 65, s. 61-68
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Tidskriftsartikel (refereegranskat)abstract
- Single-molecule fluorescence microscopy has long been appreciated as a powerful tool to study the structural dynamics that enable biological function of macromolecules. Recent years have witnessed the development of more complex single-molecule fluorescence techniques as well as powerful combinations with structural approaches to obtain mechanistic insights into the workings of various molecular machines and protein complexes. In this review, we highlight these developments that together bring us one step closer to a dynamic understanding of biological processes in atomic details.
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| 7. |
- Ban, Nenad, et al.
(författare)
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A new system for naming ribosomal proteins.
- 2014
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Ingår i: Current Opinion in Structural Biology. - : Elsevier BV. - 1879-033X .- 0959-440X. ; 24, s. 165-169
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Tidskriftsartikel (refereegranskat)abstract
- A system for naming ribosomal proteins is described that the authors intend to use in the future. They urge others to adopt it. The objective is to eliminate the confusion caused by the assignment of identical names to ribosomal proteins from different species that are unrelated in structure and function. In the system proposed here, homologous ribosomal proteins are assigned the same name, regardless of species. It is designed so that new names are similar enough to old names to be easily recognized, but are written in a format that unambiguously identifies them as 'new system' names.
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| 8. |
- Bergmann, Justin, et al.
(författare)
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Combining crystallography with quantum mechanics
- 2022
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Ingår i: Current Opinion in Structural Biology. - : Elsevier BV. - 0959-440X. ; 72, s. 18-26
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Forskningsöversikt (refereegranskat)abstract
- In standard crystallographic refinement of biomacromolecules, the crystallographic raw data are supplemented by empirical restraints that ensure that the structure makes chemical sense. These restraints are typically accurate for amino acids and nucleic acids, but less so for cofactors, substrates, inhibitors, ligands and metal sites. In quantum refinement, this potential is replaced by more accurate quantum mechanical (QM) calculations. Several implementations have been presented, differing in the level of QM and whether it is used for the entire structure or only for a site of particular interest. It has been shown that the method can improve and correct errors in crystal structures and that it can be used to determine protonation and tautomeric states of various ligands and to decide what is really seen in the structure by refining different interpretations and using standard crystallographic and QM quality measures to decide which fits the structure best.
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| 9. |
- Binder, J. L., et al.
(författare)
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AlphaFold illuminates half of the dark human proteins
- 2022
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Ingår i: Current Opinion in Structural Biology. - : Elsevier BV. - 0959-440X. ; 74
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Forskningsöversikt (refereegranskat)abstract
- We investigate the use of confidence scores to evaluate the accuracy of a given AlphaFold (AF2) protein model for drug discovery. Prediction of accuracy is improved by not considering confidence scores below 80 due to the effects of disorder. On a set of recent crystal structures, 95% are likely to have accurate folds. Conformational discordance in the training set has a much more significant effect on accuracy than sequence divergence. We propose criteria for models and residues that are possibly useful for virtual screening. Based on these criteria, AF2 provides models for half of understudied (dark) human proteins and two-thirds of residues in those models. © 2022
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| 10. |
- Bryant, Patrick
(författare)
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Deep learning for protein complex structure prediction
- 2023
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Ingår i: Current opinion in structural biology. - : Elsevier BV. - 0959-440X .- 1879-033X. ; 79
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Tidskriftsartikel (refereegranskat)abstract
- Recent developments in the structure prediction of protein complexes have resulted in accuracies rivalling experimental methods in many cases. The high accuracy is mainly observed in dimeric complexes and other problems such as protein disorder and predicting the structure of host-pathogen in-teractions remain. This review highlights the foundation for current accurate structure prediction of protein complexes and possible ways to address the remaining limitations.
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