Contact- and distance-based principal component analysis of protein dynamics.
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Summary
A systematic study of PCA using distance-based measures is presented which employs distances between Cα-atoms as well as distances between inter-residue contacts including side chains and shows that the choice of input variables may drastically influence the outcome of a PCA.
- Type
- article
- Published
- 2015-12-28
- Cited by
- 100
- References
- 66
- OpenAlex
- https://openalex.org/W26723658
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:24630157
Keywords
Bone decalcification, Clearance, H&E stain, Eosin, Medicine
References
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- JED: a Java Essential Dynamics Program for comparative analysis of protein trajectories
- Identification and Validation of Reaction Coordinates Describing Protein Functional Motion: Hierarchical Dynamics of T4 Lysozyme.
- Constructing Markov State Models to elucidate the functional conformational changes of complex biomolecules
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- Order-disorder transition of intrinsically disordered kinase inducible transactivation domain of CREB.
- Insight into novel clinical mutants of RpsA-S324F, E325K, and G341R of Mycobacterium tuberculosis associated with pyrazinamide resistance
- Azidohomoalanine: A Minimally Invasive, Versatile, and Sensitive Infrared Label in Proteins To Study Ligand Binding.
- Perspective: Identification of collective variables and metastable states of protein dynamics.
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- Automated Markov state models for molecular dynamics simulations of aggregation and self-assembly.
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- Structural and free energy landscape of novel mutations in ribosomal protein S1 (rpsA) associated with pyrazinamide resistance
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