Literature DB >> 23900782

The targets of CAPRI rounds 20-27.

Joël Janin1.   

Abstract

Eight CAPRI prediction rounds with a total of 15 targets were held in the years 2010-2012. Only five of the targets were protein assemblies comparable with those of earlier CAPRI rounds. In one target, the solvent positions at the interface had to be predicted; another was a protein-polysaccharide complex. The remainders were designed complexes issued from protein engineering experiments, and the prediction concerned either their structure or the binding affinity of the designed ligand. Affinity prediction was a new experiment in CAPRI, and a challenge for its participants. It pushed the community into developing novel procedures and score functions that will improve the performance of docking methods, help designing binders, and yield better structure-based estimates of the binding free energy of natural assemblies.
Copyright © 2013 Wiley Periodicals, Inc.

Entities:  

Keywords:  community-wide experiment; interface water binding affinity prediction; protein-polysaccharide interaction; protein-protein interaction

Mesh:

Substances:

Year:  2013        PMID: 23900782     DOI: 10.1002/prot.24375

Source DB:  PubMed          Journal:  Proteins        ISSN: 0887-3585


  6 in total

1.  Residue-centric modeling and design of saccharide and glycoconjugate structures.

Authors:  Jason W Labonte; Jared Adolf-Bryfogle; William R Schief; Jeffrey J Gray
Journal:  J Comput Chem       Date:  2016-11-30       Impact factor: 3.376

Review 2.  Prediction and redesign of protein-protein interactions.

Authors:  Rhonald C Lua; David C Marciano; Panagiotis Katsonis; Anbu K Adikesavan; Angela D Wilkins; Olivier Lichtarge
Journal:  Prog Biophys Mol Biol       Date:  2014-05-27       Impact factor: 3.667

3.  Protein-protein docking with dynamic residue protonation states.

Authors:  Krishna Praneeth Kilambi; Kavan Reddy; Jeffrey J Gray
Journal:  PLoS Comput Biol       Date:  2014-12-11       Impact factor: 4.475

4.  Addressing the Role of Conformational Diversity in Protein Structure Prediction.

Authors:  Nicolas Palopoli; Alexander Miguel Monzon; Gustavo Parisi; Maria Silvina Fornasari
Journal:  PLoS One       Date:  2016-05-09       Impact factor: 3.240

5.  SWISS-MODEL: homology modelling of protein structures and complexes.

Authors:  Andrew Waterhouse; Martino Bertoni; Stefan Bienert; Gabriel Studer; Gerardo Tauriello; Rafal Gumienny; Florian T Heer; Tjaart A P de Beer; Christine Rempfer; Lorenza Bordoli; Rosalba Lepore; Torsten Schwede
Journal:  Nucleic Acids Res       Date:  2018-07-02       Impact factor: 16.971

6.  Protein Docking Model Evaluation by Graph Neural Networks.

Authors:  Xiao Wang; Sean T Flannery; Daisuke Kihara
Journal:  Front Mol Biosci       Date:  2021-05-25
  6 in total

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