Ab initio protein structure prediction.

By Corey Hardin, Taras V. Pogorelov, Zaida Luthey-Schulten. Current Opinion in Structural Biology, 2002

345 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/d462440059c2e0457ad6bcc82a3071110924a787

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Materials Chemistry

In Molecular Biology

Citations in the corpus

Computational modeling of phosphotransfer complexes in two-component signaling. (2010, background): “Physics-based approaches (Fujitsuka et al ., 2004; Hardin et al ., 2002; Schug et al ., 2005a) struggle with the accuracy of the underlying force-fields, especially for mixed a -helical/ b -sheet structures (Best et al ., 2008).”
In silico methods and tools for drug discovery (2021, methodology): “If appropriate template structures are not available, an ab initio protein structure modeling approach can be utilized [140].”
Potential functions for hydrogen bonds in protein structure prediction and design. (2005, methodology): “…minima or molecular dynamics (MD) simulations, which employ Newton’s laws to construct dynamical molecular trajectories (Hansson et al., 2002)]; and (c) postprocessing of an ensemble of computationally predicted models (decoys) occupying local minima on the energy landscape (Hardin et al., 2002).”
Computational methods in drug discovery (2016, methodology): “Several methods have been used for protein structure prediction including homology modeling [26,27], threading approaches [28], and ab initio folding [29,30].”
Strategies and molecular tools to fight antimicrobial resistance: resistome, transcriptome, and antimicrobial peptides (2013, methodology): “Prediction ab initio (de novo) makes use of the energy minimized functions and research of spatial conformations that the target can take, and this is important for the use of force fields and methods of molecular dynamics and Monte Carlo simulations (Lee et al., 2009).”
ModeRNA: a tool for comparative modeling of RNA 3D structure (2011, methodology): “The second approach for structure prediction is ab initio modeling based on biophysical rules, which simulates the folding process in search of the conformation with the minimal free energy [review: (27)].”
Computational protein structure refinement: Almost there, yet still so far to go (2017, background): “10,11 14 While much has been learned at the fundamental level about protein structures and the folding process, 13 pure ab initio methods that do not use any information from known structures largely fail to accurately and reliably predict the structures of all but very small proteins.”