“NACEN” is a R package that could provide the construction and analysis for node-weighted amino acids contact energy network (NACEN).

1. System Requirements and Installation

1). Requirements

The main requirement for NACEN is a working installation of R >= 3.2.0 on Windows. The package also requires the bio3d and igraph R packages. The additional program DSSP 3.0 is also required, and it’s already included in the installation package. Or You could download them from http://swift.cmbi.ru.nl/gv/dssp/.

2). Download

The NACEN R package, required tool and example data could be download here.

3). Installation

Install “NACEN” package from local

install.packages("E:/NACEN/NACEN_0.1.0.tar.gz", repos = NULL, type = "source")

2. Examples

1). NACEN Construction

a. Construct unweighted AACEN

If we set WeightType = ‘none’, the function will just construct the AACEN without node weights.

library(NACEN)
dsspfile <- "dssp-3.0.0.exe" #here we put DSSP programm in the path "E:\NACEN\"
Net1 <- NACENConstructor('1vie',WeightType = "none",exefile = dsspfile)
##   Note: Accessing on-line PDB file

Net1 is a list which consists of network adjacent matrix (AM), nodes weights vector (NodeWeights), and data frame (PDBInform) about the information of backbone residues

b. Construct NACEN by select default features in the package as node weights, such as polarity.

Net2 <- NACENConstructor(PDBFile='E:/NACEN/1vie.pdb',WeightType = "Polarity",exefile = dsspfile,plotflag=T)
## [1] "The network figure is saved in your current working directory"
dim(Net2$AM) #AM's dimensions
## [1] 60 60
head(Net2$PDBInform) # backbone residues information
##    type eleno elety  alt resid chain resno insert      x      y      z o
## 2  ATOM     2    CA <NA>   PRO     A    19   <NA> 40.866 32.472 51.115 1
## 9  ATOM     9    CA <NA>   SER     A    20   <NA> 42.608 30.280 53.665 1
## 15 ATOM    15    CA <NA>   ASN     A    21   <NA> 44.003 28.417 50.726 1
## 23 ATOM    23    CA <NA>   ALA     A    22   <NA> 43.887 30.181 47.234 1
## 28 ATOM    28    CA <NA>   THR     A    23   <NA> 46.959 30.799 45.093 1
## 35 ATOM    35    CA <NA>   PHE     A    24   <NA> 46.004 34.310 44.345 1
##         b segid elesy charge SS ACC    Phi   PSi chain.1 resno.1
## 2  100.00  <NA>     C   <NA>  X 125  360.0 148.5       A      19
## 9   74.28  <NA>     C   <NA>  X 135  -54.1  14.3       A      20
## 15  45.38  <NA>     C   <NA>  S 134 -156.6 -27.4       A      21
## 23  15.62  <NA>     C   <NA>  X  24  -48.9 145.9       A      22
## 28  14.99  <NA>     C   <NA>  S  81  -71.1 -38.2       A      23
## 35  11.51  <NA>     C   <NA>  S  17 -123.8 164.7       A      24
Net2$NodeWeights #Node weights
##         P         S         N         A         T         F         G 
## 0.3202934 0.1515892 0.3276284 0.1124694 0.2640587 0.7090465 0.0000000 
##         M         G         D         R         V         R         K 
## 0.5403423 0.0000000 0.2567237 0.7114914 0.3422983 0.7114914 0.5354523 
##         K         S         G         A         A         W         Q 
## 0.5354523 0.1515892 0.0000000 0.1124694 0.1124694 1.0000000 0.4400978 
##         G         Q         I         V         G         W         Y 
## 0.0000000 0.4400978 0.4547677 0.3422983 0.0000000 1.0000000 0.7286064 
##         C         T         N         L         T         P         E 
## 0.3129584 0.2640587 0.3276284 0.4547677 0.2640587 0.3202934 0.3691932 
##         G         Y         A         V         E         S         E 
## 0.0000000 0.7286064 0.1124694 0.3422983 0.3691932 0.1515892 0.3691932 
##         A         H         P         G         S         V         Q 
## 0.1124694 0.5623472 0.3202934 0.0000000 0.1515892 0.3422983 0.4400978 
##         I         Y         P         V         A         A         L 
## 0.4547677 0.7286064 0.3202934 0.3422983 0.1124694 0.1124694 0.4547677 
##         E         R         I         N 
## 0.3691932 0.7114914 0.4547677 0.3276284

c. Construct NACEN by user defined weights

Set WeightType=“others”, and give the file path of node weights

Net3 <- NACENConstructor(PDBFile='E:/NACEN/1vie.pdb',WeightType = "others",exefile = dsspfile,WeightFile="E:/NACEN/Nodes.txt")

2). NACEN Analysis

NACEAnanlyzer could calculate the unweighted degree, betweenness and closeness and corresponding node-weighted degree, betweenness and closeness.

NetP <- NACENAnalyzer(Net2$AM,Net2$NodeWeights)
head(NetP$NetP)
##                ID chain Resid Res K   B           C         Kw         Bw
## A:19:PRO A:19:PRO     A    19 PRO 1   0 0.002145923 0.00000000 0.00000000
## A:20:SER A:20:SER     A    20 SER 2  58 0.002450980 0.01378084 0.01794931
## A:21:ASN A:21:ASN     A    21 ASN 2 114 0.002840909 0.02978440 0.07624962
## A:22:ALA A:22:ALA     A    22 ALA 3 168 0.003355705 0.02044899 0.03857404
## A:23:THR A:23:THR     A    23 THR 2   0 0.003322259 0.02400533 0.00000000
## A:24:PHE A:24:PHE     A    24 PHE 3 270 0.004048583 0.12891754 0.39083170
##                  Cw
## A:19:PRO 0.00000000
## A:20:SER 0.01053376
## A:21:ASN 0.05186696
## A:22:ALA 0.03099379
## A:23:THR 0.07075628
## A:24:PHE 0.30730452
head(NetP$Edgelist)
##      [,1]       [,2]      
## [1,] "A:19:PRO" "A:20:SER"
## [2,] "A:20:SER" "A:21:ASN"
## [3,] "A:21:ASN" "A:22:ALA"
## [4,] "A:22:ALA" "A:23:THR"
## [5,] "A:22:ALA" "A:24:PHE"
## [6,] "A:23:THR" "A:24:PHE"

3). NACEN Visualization

The visualization of NACEN could be performed by plotNACEN function or by set the parameter plotflag=T in the function NACENConstructor which will save the figure in current work path.

plotNACEN(Net2)

4). Node Weights selection from AAIndex database

PDBresidues <- bio3d::aa321(Net2$PDBInform$resid)
NodeWeights <- NodeW(PDBresidues,WeightType="Mass")
NodeWeights <- NodeW(PDBresidues,WeightType="CHAM820101")

NodeW provides node weights selection from AAIndex database. WeightType could be the ID in the database.

Copyright 2018 Center for Systems Biology, Soochow University. All Rights Reserved.