Ab initio protein structure prediction: progress and prospects.

By Richard Bonneau, David Baker. 2001

337 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology

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Citations in the corpus

Critical Assessment of Methods of Protein Structure Prediction (CASP) – Round XII (2017, background): “In the previous CASP (11), there were just 2 targets where new approaches to this problem 8 resulted in accurate models for relatively large structures for which no template was available.”
Statistical potentials for fold assessment (2002, neutral): “The fold has to be assessed almost invariably for all of the models predicted by ab initio methods (Jones 1997; Ortiz et al. 1999; Xia et al. 2000; Bonneau and Baker 2001; Pillardy et al. 2001) and threading of sequences into structures (Bowie et al.”
Experimental accuracy in protein structure refinement via molecular dynamics simulations (2018, background): “A conceptually simple approach is ab initio folding from extended chains to follow the folding process based on physical laws (4).”
Protease degradomics: A new challenge for proteomics (2002, methodology): “, or by using a combination of homology modelling and ab initio predictions that aim to predict the three-dimensional structure of a protein from its amino-acid sequenc”
Computational protein structure refinement: Almost there, yet still so far to go (2017, background): “One idea to overcome this conundrum may be the simultaneous use of multiple restraints 148,192 and/or adaptive restraints 15,89,90 to limit sampling while still being able to reach the native state.”
MODBASE: a database of annotated comparative protein structure models and associated resources (2005, methodology): “The first class of methods, de novo or ab initio methods, predicts the structure from sequence alone, without relying on similarity at the fold level between the modeled sequence and any of the known structures (8).”
CavitySpace: A Database of Potential Ligand Binding Sites in the Human Proteome (2022, background): “Fortunately, protein structure prediction approaches have made great progress in the past several years [24–26].”
Chemical shift-based methods in NMR structure determination (2018, methodology): “Structure prediction methods have shown great success for small to medium sized proteins (<150 residues) using various strategies, including ab initio [48,49], comparative modeling [50], fold prediction and threading [51].”
Structure Refinement of Membrane Proteins via Molecular Dynamics Simulations (2018, background): “Although these methods have succeeded in some cases, they remain computationally expensive and generally do not provide accurate predictions for most proteins.(11) Much more successful has been the use of structural templates from known structures.”