References
Webserver
- Christoffer, C., Chen, S., Bharadwaj, V., Aderinwale, T., Kumar, V., Hormati, M., and Kihara, D. (2021). LZerD webserver for pairwise and multiple protein docking. Nucleic Acids Research, 49(W1), W359–W365.
- Christoffer, C., Bharadwaj, V., Luu, R., and Kihara, D. (2021). LZerD protein-protein docking webserver enhanced with de novo structure prediction . Frontiers in Molecular Biosciences, accepted.
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.
- Rosetta REF2015
Park, H., Bradley, P., Greisen, P., Jr., Liu, Y., Mulligan, V.K., Kim, D.E., Baker, D. and DiMaio, F. (2016). Simultaneous Optimization of Biomolecular Energy Functions on Features from Small Molecules and Macromolecules. Journal of Chemical Theory and Computation 12, 6201-6212.
Protein Structure Prediction (single-chain)
- AttentiveDist
Jain, A., Terashi, G., Kagaya, Y., Subramaniya, S., Christoffer, C., and Kihara, D. (2021). Analyzing effect of quadruple multiple sequence alignments on deep learning based protein inter-residue distance prediction. Scientific Reports 11, 7574 (2021)