The challenge of modeling protein assemblies: the CASP12‐CAPRI experiment

By Marc F. Lensink, S. Velankar, Minkyung Baek, Lim Heo, Chaok Seok, Shoshana J. Wodak. 2018

84 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology

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

1. Andriy Kryshtafovych
2. Torsten Schwede
3. Krzysztof Fidelis
4. Yang Zhang
5. Anna Tramontano
6. John Moult
7. Petras J. Kundrotas
8. Ilya A. Vakser

In Molecular Biology

1. Andriy Kryshtafovych
2. Torsten Schwede
3. Yang Zhang
4. Krzysztof Fidelis
5. Anna Tramontano
6. John Moult
7. Petras J. Kundrotas
8. Ilya A. Vakser

Citations in the corpus

• Critical Assessment of Methods of Protein Structure Prediction (CASP) – Round XII (2017, background): “37 A total of 30 oligomeric targets were suitable for assembly prediction and assessment: 8 heteromeric assemblies and 22 homo-oligomeric targets.”
• Protein Data Bank: the single global archive for 3D macromolecular structure data (2018, methodology): “Release of PDB data in two phases is intended to assist the computational biology community in operating various prediction challenges, including CASP (32), CAPRI (33), CAMEO (34) and D3R (35).”
• Performance and its limits in rigid body protein-protein docking (2020, unknown): “based on the top 5 rather than top 10 predictions (Lensink et al., 2019b; Lensink et al., 2018; Lensink et al., 2017).”
• Application of docking methodologies to modeled proteins (2020, methodology): “26 Combining free and comparative docking methods yields more successful predictions than either method alone.”
• Assessment of the CASP14 Assembly Predictions (2021, methodology): “44 These predictions came from a classical template-based approach (established by the consecutive use of HHPred 28,29 and Modeller 45 ).”
• InterEvDock2: an expanded server for protein docking using evolutionary and biological information from homology models and multimeric inputs (2018, background): “Although the InterEvDock2 pipeline was not specifically designed to handle homo-oligomeric docking, we were also among the highest ranking groups in the two joint CASPCAPRI experiments involving mostly predictions of homodimers (46,47).”
• The HDOCK server for integrated protein–protein docking (2020, methodology): “…as building structures from sequences, incorporating binding interface information and running docking commands, although our docking protocol achieved an excellent performance in the multimeric protein structure prediction in the community-wide CASP11-CAPRI and CASP12-CAPRI experiments 21,25,26 .”
• Small angle X-ray scattering and cross-linking for data assisted protein structure prediction in CASP 12 with prospects for improved accuracy (2018, methodology): “More recently CASP began collaborating with CAPRI, 4 to address difficulties in predicting interfaces, multimeric structure, and formation.”
• What Method to Use for Protein-Protein Docking? (2019, methodology): “Second, we discuss the shift toward template-based docking, primarily considering the prediction of homo-oligomers, by looking at the results of the latest structure prediction experiments called CASP11-CAPRI [4], and CASP12-CAPRI [5].”