ArticleActa crystallographica. Section D, Structural biology2021
Adaptive Cartesian and torsional restraints for interactive model rebuilding.
Article in Acta crystallographica. Section D, Structural biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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11 citing papers in PubMed.
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- 2.7 Å cryo-EM structure of human telomerase H/ACA ribonucleoprotein.Nature communications · 2024Article
- Putting AlphaFold models to work with phenix.process_predicted_model and ISOLDE.Acta crystallographica. Section D, Structural biology · 2022Article
- Activation of the human insulin receptor by non-insulin-related peptides.Nature communications · 2022Article
- Cryo-EM reveals mechanisms of angiotensin I-converting enzyme allostery and dimerization.The EMBO journal · 2022Article
- How insulin-like growth factor I binds to a hybrid insulin receptor type 1 insulin-like growth factor receptor.Structure (London, England : 1993) · 2022Article
- Structural basis of human telomerase recruitment by TPP1-POT1.Science (New York, N.Y.) · 2022Article
- The structure of the bacterial DNA segregation ATPase filament reveals the conformational plasticity of ParA upon DNA binding.Nature communications · 2021Article
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2 authors.
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Abstract
When building atomic models into weak and/or low-resolution density, a common strategy is to restrain their conformation to that of a higher resolution model of the same or similar sequence. When doing so, it is important to avoid over-restraining to the reference model in the face of disagreement with the experimental data. The most common strategy for this is the use of `top-out' potentials. These act like simple harmonic restraints within a defined range, but gradually weaken when the deviation between the model and reference grows beyond that range. In each current implementation the rate at which the potential flattens at large deviations follows a fixed form, although the form chosen varies among implementations. A restraint potential with a tuneable rate of flattening would provide greater flexibility to encode the confidence in any given restraint. Here, two new such potentials are described: a Cartesian distance restraint derived from a recent generalization of common loss functions and a periodic torsion restraint based on a renormalization of the von Mises distribution. Further, their implementation as user-adjustable/switchable restraints in ISOLDE is described and their use in some real-world examples is demonstrated.
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