READ_ME
##################################################### ## ## ## READ_ME_FAA.txt January 4, 2016 ## ## ## ##################################################### Description; Tools and functions for Fragment Assembly Approach URL; http://dmar.riken.jp/Rscripts/ Depends; R (https://www.r-project.org/) Bioclipse Scripting Language (http://bioclipse.net/) Gaussian09 (http://www.gaussian.com/) Reference; Ito, K., Tsutsumi, Y., Date, Y., Kikuchi, J. ACS Chem. Biol. 11, 1030−1038 (2016). [1] Alignment of NMR signals (Under construction) Please type these codes on R console, source("http://emar.riken.jp/FAA/TesHistAli.R") # download function source("http://emar.riken.jp/FAA/HistAli.R") # download function TesHistAli(HSQC,HSQCTOCSY,COSY1H,COSY13C,0.01,0.01,noiseH,noiseC,1024) # example analysis RES <- HistAli(HSQC,HSQCTOCSY,COSY1H,COSY13C,bwH,bwC,noiseH,noiseC,N) # example analysis source("http://emar.riken.jp/FAA/ProjAli.R") # download function RES <- ProjAli(HSQC,HSQCTOCSY,COSY1H,COSY13C,Hali,Cali) # example analysis [2] Automatic chain assignment based on network theory Please type these codes on R console, source("http://emar.riken.jp/FAA/NMRcorDATA.R") # download example data set source("http://emar.riken.jp/FAA/MultiNetv11.R") # download function RES <- MultiNetv11(HSQC,HSQCTOCSY,COSY1H,COSY13C,0.001,0.001) # example analysis RES$GroupCount # separated peaks to group RES$RESULTcoordinate # chemical shift of each group RES$Connect4C # correlation with quaternary carbon # the number is linked with $RESULTcoordinate [3] Structute estimation based on graph theory Partial structures are estimated by Maximum Common Substructure (MCS) analysis. "MCS_example_code" is an example file of Javascript for MCS using 7 compounds. MCS is calculated by Bioclipse Scripting Language with CDK library. Cluster analysis using the Levenshtein distance of the Hierarchical Organization of Spherical Environments (HOSE) code of the partial structure extracts matching compounds. Please type these codes on R console, source("http://emar.riken.jp/FAA/HOSEdata.R") # download example data set source("http://emar.riken.jp/FAA/Clus_HOSE.R") # download function Clus_HOSE(HOSEdata) # example analysis [4] Dihedral angle difference root mean square (RMS) comparison method Please type these codes on R console, source("http://emar.riken.jp/FAA/angle3D.R") # download function for calculation of angle in xyz source("http://emar.riken.jp/FAA/dRMS.R") # download function for dihedral angle difference RMS comparison source("http://emar.riken.jp/FAA/xyzEXP.R") # download function for extraction of coordinate source("http://emar.riken.jp/FAA/All_angle.R") # download function for calculation of all angles source("http://emar.riken.jp/FAA/REF.R") # download example data set of 4 points of dihedral angle source("http://emar.riken.jp/FAA/Rawdata.R") # download example data set of all coordinates after grid searching source("http://emar.riken.jp/FAA/energy.R") # download example data set of potential energy of all coordinates All_angle(REF, Rawdata, energy) # example analysis RES <- dRMS(dDATA, dDATA2) # example analysis xyzEXP(1) # example analysis [5] Chemical shift calculation based on quantum chemistry Theoretical chemical shift is calculated by using Gaussian09. "DSS.com" and "DSS_ion.com" are imput files as reference material. "Formate.com" and "Formate_ion.com" are imput files as example of metabolite. These files are made for optimization and chemical shift calculation with PCM method.