RDOCK: Refinement of rigid‐body protein docking predictions
By Li Li, Rong Chen, Zhiping Weng. Proteins: Structure, Function, and Bioinformatics, 2003
328 citations recorded by the source corpus.
Subfields: Materials Chemistry, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/69b3693504c31cbef176f14cdd54af0aab2bdef3
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
- D. Ritchie
- Shengyou Huang
- Alexandre M. J. J. Bonvin
- Xiaoqin Zou
- Brian G. Pierce
- Ruth Nussinov
- Haim J. Wolfson
- Zhiping Weng
In Molecular Biology
- Shengyou Huang
- Xiaoqin Zou
- Alexandre M. J. J. Bonvin
- D. Ritchie
- Haim J. Wolfson
- Ruth Nussinov
- Nelly Andrusier
- Brian G. Pierce
Citations in the corpus
- PIPER: An FFT‐based protein docking program with pairwise potentials (2006, neutral): “10,13,14 The discrimination between near-native and other structures can be further improved by clustering methods.”
- ZRANK: Reranking protein docking predictions with an optimized energy function (2007, methodology): “18 It uses the CHARMM program 19 to perform energy minimization on the top ZDOCK predictions (the top 2000 is recommended), and reranks these predictions using desolvation and electrostatics.”
- FireDock: Fast interaction refinement in molecular docking (2007, background): “31,33,35,58 This happens because the ligand reaches the binding site of the receptor from the broad neighborhood region.”
- FireDock: a web server for fast interaction refinement in molecular docking (2008, methodology): “The minimization is performed using methods such as Steepest Descent (17), Newton–Raphson (18,19), Quasi-Newton (12,16) and more.”
- Recent progress and future directions in protein-protein docking. (2008, methodology): “…as threading, phylogenetic profiling, gene neighbourhood and gene fusion analysis, and in silico two-hybrid methods are being used with increasing success to predict PPIs directly from gene sequences of yeast and other organisms (for recent reviews see e.g., references [8] [9] [10] [11] [12] [13]).”
- An iterative knowledge‐based scoring function for protein–protein recognition (2008, methodology): “To keep the consistency with the literature,71,72 the success criterion for binding mode prediction used in the ZDOCK studies was adopted for our ZDOCK decoy tests.”
- Flexible protein-protein docking. (2006, positive): “This typically does not lead to any significant improvement in RMSD from the target structure, but rather is meant to remove clashes and improve the energetics, which can have a significant impact on the scoring performance [28].”