Contact Potential for Structure Prediction of Proteins and Protein Complexes from Potts Model.
By Ivan V. Anishchenko, Petras J. Kundrotas, Ilya A. Vakser. 2018
23 citations recorded by the source corpus.
The energy function is the key component of protein modeling methodology. This work presents a semianalytical approach to the development of contact potentials for protein structure modeling. Residue-residue and atom-atom contact energies were derived by maximizing the probability of observing native sequences in a nonredundant set of protein structures. The optimization task was formulated as an inverse statistical mechanics problem applied to the Potts model. Its solution by pseudolikelihood maximization provides consistent estimates of coupling constants at atomic and residue levels. The best performance was achieved when interacting atoms were grouped according to their physicochemical properties. For individual protein structures, the performance of the contact potentials in distinguishing near-native structures from the decoys is similar to the top-performing scoring functions. The potentials also yielded significant improvement in the protein docking success rates. The potentials recapitulated experimentally determined protein stability changes upon point mutations and protein-protein binding affinities. The approach offers a different perspective on knowledge-based potentials and may serve as the basis for their further development.
Subfields: Molecular Biology, Spectroscopy
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Molecular Biology
- Arne Elofsson
- Gabriele Pozzati
- Petras J. Kundrotas
- Patrick Bryant
- Taras Dauzhenka
- Michael J.E. Sternberg
- Amar Singh
- Ilya A. Vakser
In Spectroscopy
- Gabriele Pozzati
- Arne Elofsson
- Patrick Bryant
- Russ B. Altman
- Michael J.E. Sternberg
- Raphael R. Eguchi
- Namrata Anand-Achim
- Po-Ssu Huang
Citations in the corpus
- Improved prediction of protein-protein interactions using AlphaFold2 (2021, methodology): “The atom-atom contact energy AACE18 is used to score and rank all poses, as this has been shown to provide better results than shape-complementarity alone 47 .”
- Application of docking methodologies to modeled proteins (2020, methodology): “44 Template based docking was performed by the full-structure alignment protocol.”
- Protein sequence design with a learned potential (2020, background): “Most relevant to this work are statistical potentials which explicitly model local sequence and structure features at residue positions to perform sequence design [55, 57, 58, 69, 70, 71].”