Write 1 Bin

來自引述 WCN 的 paper - Using catalytic atom maps to predict .........

Seven bins for each data set 

PDB dataset path

/home/database/rcsb/data/biounit/coordinates/divided

aggregation region

Find the aggregation region in thermophilic protein ( PDB )

1. WCN
2. Hydrophobic
3. Conservation
4. B-factor
5. CN (cutoff 9 angstrom)
6. RSA

催化 catalytic site

結構相關因子:
pocket,  RSA, rigidity, packing density (WCN),
fixed geometry (structure conserved , distance, angle -> function ) 
 
降低活化能 free energy barrier
加速化學反應




ref.
Coupling between Catalytic Site and Collective Dynamics: A Requirement for Mechanochemical Activity of Enzymes

Zhiping Weng

Structure, function, and evolution of transient and obligate protein–protein interactions  Link

Recent analyses of high-throughput protein interaction data coupled with large-scale investigations of evolutionary properties of interaction networks have left some unanswered questions. To what extent do protein interactions act as constraints during evolution of the protein sequence? How does the type of interaction, specifically transient or obligate, play into these constraints? Are the mutations in the binding site of an interacting protein correlated with mutations in the binding site of its partner? We address these and other questions by relying on a carefully curated dataset of protein complex structures. Results point to the importance of distinguishing between transient and obligate interactions. We conclude that residues in the interfaces of obligate complexes tend to evolve at a relatively slower rate, allowing them to coevolve with their interacting partners. In contrast, the plasticity inherent in transient interactions leads to an increased rate of substitution for the interface residues and leaves little or no evidence of correlated mutations across the interface.

LabLink

ggplot2 Shapes and line types

Link

Note that the filled symbols 15-18 often render without proper anti-aliasing; they can appear jagged, pixelated, and not properly centered. Use symbols 19 and 21-25 to avoid these problems. For symbols 21-25 to appear solid, you will also need to specify a fill (bg) color that is the same as the outline color (col); otherwise they will be hollow.

Use the pch option to set the shape, and use lty and lwd to 

set the line type and width. The line type can be specified 

by name or by number. 

set.seed(331)

# Plot some points with lines
# Set up the plotting area
plot(NA, xlim=c(1,4), ylim=c(0,1))

# Plot solid circles with solid lines
points(1:4, runif(4), type="b", pch=19)
# Add open squares with dashed line, with heavier line width
points(1:4, runif(4), type="b", pch=0,  lty=2, lwd=3)

points(1:4, runif(4), type="b", pch=23,   # Diamond shape
       lty="dotted", cex=2,               # Dotted line, double-size shapes
       col="#000099", bg="#FF6666")       # blue line, red fill

ggplot2 語法 1

原著  Link

1. 下面用ggplot2包內帶的汽車測試數據（mpg）來舉個例子，用到的三個變量分別是
     發動機容量(displ)、
     高速公路上的每加侖行駛里數(hwy)、
     汽缸數目(cyl)
     
首先加載ggplot2包，然後用ggplot定義第一層即數據來源。 其中aes參數非常關鍵，它將displ映射到X軸，將hwy映射到Y軸，將cyl變為分類數據後映射為不同的顏色。 然後使用+號添加了兩個新的圖層，第二層是加上了散點，第三層是加上了loess平滑曲線。

library(ggplot2)
p <- ggplot(data=mpg, aes(x=displ, y=hwy, colour=factor(cyl)))
p + geom_point() + geom_smooth()

上圖是對幾種不同汽缸的數據分別平滑，如果需要對整體數據進行平滑，可將colour參數設置在散點圖層內而非第一層，這樣第三層的平滑圖形就不會受到colour參數的影響。

p <- ggplot ( mpg , aes ( x=displ , y=hwy ) )
p + geom_point ( aes ( colour= factor ( cyl ) ) ) + geom_smooth ( )