References
LZerD
- Venkatraman, V., Yang, Y.D., Sael, L., and Kihara, D. (2009). Protein-protein docking using region-based 3D Zernike descriptors. BMC Bioinformatics 10, 407.
- Esquivel-Rodriguez, J., Filos-Gonzalez, V., Li, B., and Kihara, D. (2014). Pairwise and Multimeric Protein–Protein Docking Using the LZerD Program Suite. In Methods in Molecular Biology, (Springer New York), pp. 209–234.
Multi-LZerD
- Esquivel-Rodríguez, J., Yang, Y.D., and Kihara, D. (2012). Multi-LZerD: multiple protein docking for asymmetric complexes. Proteins: Structure, Function, and Bioinformatics 80, 1818-1833.
- Esquivel-Rodriguez, J., Filos-Gonzalez, V., Li, B., and Kihara, D. (2014). Pairwise and Multimeric Protein–Protein Docking Using the LZerD Program Suite. In Methods in Molecular Biology, (Springer New York), pp. 209–234.
CAPRI Performance Evaluation
- Lensink, M.F., Brysbaert, G., Nadzirin, N., Velankar, S., Chaleil, R.A.G., Gerguri, T., Bates, P.A., Laine, E., Carbone, A., Grudinin, S., et al. (2019). Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment. Proteins: Structure, Function, and Bioinformatics 87, 1200–1221.
- Lensink, M.F., Velankar, S., Baek, M., Heo, L., Seok, C., and Wodak, S.J. (2017). The challenge of modeling protein assemblies: the CASP12-CAPRI experiment. Proteins: Structure, Function, and Bioinformatics 86, 257–273.
- Lensink, M.F., Velankar, S., and Wodak, S.J. (2016). Modeling protein-protein and protein-peptide complexes: CAPRI 6th edition. Proteins: Structure, Function, and Bioinformatics 85, 359–377.
Analysis of Our Performance
- Christoffer, C., Terashi, G., Shin, W., Aderinwale, T., Maddhuri Venkata Subramaniya, S.R., Peterson, L., Verburgt, J., and Kihara, D. (2019). Performance and enhancement of the LZerD protein assembly pipeline in CAPRI 38-46. Proteins: Structure, Function, and Bioinformatics.
- Peterson, L.X., Shin, W.-H., Kim, H., and Kihara, D. (2017). Improved performance in CAPRI round 37 using LZerD docking and template-based modeling with combined scoring functions. Proteins: Structure, Function, and Bioinformatics 86, 311–320.
- Peterson, L.X., Kim, H., Esquivel-Rodriguez, J., Roy, A., Han, X., Shin, W.-H., Zhang, J., Terashi, G., Lee, M., and Kihara, D. (2016). Human and server docking prediction for CAPRI round 30-35 using LZerD with combined scoring functions. Proteins: Structure, Function, and Bioinformatics 85, 513–527.
Scoring Functions
- GOAP
Zhou, H., and Skolnick, J. (2011). GOAP: A Generalized Orientation-Dependent, All-Atom Statistical Potential for Protein Structure Prediction. Biophysical Journal 101, 2043–2052.
- DFIRE
Zhou, H., and Zhou, Y. (2009). Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction. Protein Science 11, 2714–2726.
- ITScore
Huang, S.-Y., and Zou, X. (2011). Statistical mechanics-based method to extract atomic distance-dependent potentials from protein structures. Proteins: Structure, Function, and Bioinformatics 79, 2648–2661.