A hierarchical approach to all‐atom protein loop prediction

By Matthew P. Jacobson, David L. Pincus, Chaya Rapp, T. Day, Barry Honig, David E. Shaw, Richard A. Friesner. 2004

2,320 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology

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Citations in the corpus

D3R Grand Challenge 2: Blind Prediction of Protein-Ligand Poses, Affinity Rankings, and Relative Binding Free Energies (2017, methodology): “…are based on a binding site alignment script provided by the Maestro Prime Suite [27] ( align-binding-sites ) that performs a secondary structure alignment of the full protein followed by an alignment using the binding site Cα atoms belonging to residues within 5 Å of the ligand atoms [28, 29].”
Remdesivir is a direct-acting antiviral that inhibits RNA-dependent RNA polymerase from severe acute respiratory syndrome coronavirus 2 with high potency (2020, methodology): “Homology models of other coronaviruses, including SARS and MERS, were generated from this model with Prime.”
Analysis and Modeling of the Variable Region of Camelid Single Domain Antibodies (2011, methodology): “, Protein Local Optimization Program (16) samples 2 loop conformations up to 10(6), where n is the loop length).”
Protein structure modeling with MODELLER. (2014, methodology): “, insertions or loops) are among the most difficult regions to model(13,51-53).”
Comparative Protein Structure Modeling Using MODELLER (2007, methodology): “…(Matsumoto et al., 1995); in facilitating molecular replacement in X-ray structure determination (Howell et al., 1992); in reﬁning models based on NMR constraints (Modi et al., 1996); in testing and improving a sequence-structure alignment (Wolf et al., 1998); in annotating single nucleotide…”
Fast Protein Loop Sampling and Structure Prediction Using Distance-Guided Sequential Chain-Growth Monte Carlo Method (2014, neutral): “Currently, the hierarchical approach of the Protein Local Optimization Program (PLOP) [13,14,23] gives excellent accuracy in protein loop modeling, but requires significant computational time.”
SnugDock: Paratope Structural Optimization during Antibody-Antigen Docking Compensates for Errors in Antibody Homology Models (2010, background): “We identified 15 antibodies with known complex structures and H3 loop lengths between 7 and 11 residues, the range where loop structure prediction is of medium accuracy [27,37].”
Computational protein structure refinement: Almost there, yet still so far to go (2017, methodology): “85, 132,160 – 165 Other methods sample conformations either via the direct replacement of fragments from a library, often via Monte Carlo (MC) sampling, 53,158,166 or by guiding MD sampling by constraints from such fragments.”
Refinement of unreliable local regions in template‐based protein models (2012, background): “Considering the previously reported successes in the native loop reconstruction,4–6 a major factor limiting the performance of refinement seems to be inaccuracy of the template-based model that provides the framework structure.”