CorNet: Assigning function to networks of co-evolving residues by automated literature mining
نویسندگان
چکیده
CorNet is a web-based tool for the analysis of co-evolving residue positions in protein super-family sequence alignments. CorNet projects external information such as mutation data extracted from literature on interactively displayed groups of co-evolving residue positions to shed light on the functions associated with these groups and the residues in them. We used CorNet to analyse six enzyme super-families and found that groups of strongly co-evolving residues tend to consist of residues involved in a same function such as activity, specificity, co-factor binding, or enantioselectivity. This finding allows to assign a function to residues for which no data is available yet in the literature. A mutant library was designed to mutate residues observed in a group of co-evolving residues predicted to be involved in enantioselectivity, but for which no literature data is available yet. The resulting set of mutations indeed showed many instances of increased enantioselectivity.
منابع مشابه
Cost Function Modelling for Semi-automated SC, RTG and Automated and Semi-automated RMG Container Yard Operating Systems
This study analyses the concept of cost functions for semi-automated Straddle Carrier (SC), Rubber Tyred Gantry (RTG) and automated Rail Mounted Gantry (RMG) container yard operating cranes. It develops a generic cost based model for a pair-wise comparison, analysis and evaluation of economic efficiency and effectiveness of container yard equipment to be used for decision-making by terminal pla...
متن کاملA Laboratory Study on Stress Dependency of Joint Transmissivity and its Modeling with Neural Networks, Fuzzy Method and Regression Analysis
Correct estimation of water inflow into underground excavations can decrease safety risks and associated costs. Researchers have proposed different methods to asses this value. It has been proved that water transmissivity of a rock joint is a function of factors, such as normal stress, joint roughness and its size and water pressure therefore, a laboratory setup was proposed to quantitatively m...
متن کاملOptimization of the Cost Function in the Drilling of Oil Well Network by Balas Algorithm
The most costly operation in the oil exploration is the well network drilling. One of the most effective ways to reduce the cost of drilling networks is decreasing the number of the required wells by selecting the optimum situation of the rig placement. In this paper, Balas algorithm is used as a model for optimizing the cost function in oil well network, where the vertical and directional dril...
متن کاملGenetic program based data mining of fuzzy decision trees and methods of improving convergence and reducing bloat
A data mining procedure for automatic determination of fuzzy decision tree structure using a genetic program (GP) is discussed. A GP is an algorithm that evolves other algorithms or mathematical expressions. Innovative methods for accelerating convergence of the data mining procedure and reducing bloat are given. In genetic programming, bloat refers to excessive tree growth. It has been observe...
متن کامل