CDPro_software_CDProSoftware_源码_cdpro软件资源-CSDN文库

共96个文件

smp：14个

htm：8个

out：8个

software

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CDPro.zip （96个子文件）

圆二色处理：CDPro

CDDATA.42 23KB

SSDATA.43 3KB

BASIS.PG 23KB

input 1KB

run_slcn.bat 445B

SSDATA.P2 2KB

betaplus 262B

Input.htm 9KB

CDDATA.48 26KB

main.html 7KB

selcon3.out 14KB

SSDATA.CA 8KB

ProtSS.out 10KB

cdsstr.out 8KB

RunCDPro.html 342B

top.htm 3KB

CLUSTMP 5KB

[muchong.com]CDPro.zip 884KB

ProtSS.SMP 8KB

betaalfa 262B

Selcon3.SMP 82KB

betaslsh 263B

CDDATA.43 25KB

CALCCD.SMP 2KB

CLUSTER.smp 2KB

run_edit.bat 452B

mainrun.html 6KB

JUNK 1KB

SSDATA.DN 471B

CDDATA.37 21KB

CDDATA.AA 5KB

CDDATA.23 11KB

SUMMARY.PG 18KB

CLUSTER.EXE 203KB

CONTIN.OUT 106KB

dentslsh 262B

PAM40.INP 899B

slshplus 266B

Output.htm 52KB

CalcCD.OUT 2KB

BASIS 28KB

index.html 327B

Continll.SMP 32KB

crdata.inp 1KB

toprun.htm 3KB

CDDATA.CA 30KB

Input.SMP 2KB

run_cntn.bat 417B

CDDATA.P2 21KB

SSDATA.37 2KB

BASIS.SMP 20KB

crdata.out 830B

continll.out 10KB

Guide.htm 13KB

CRDATA.smp 5KB

SSDATA.AA 520B

SSDATA.42 3KB

SSDATA.23 1KB

SSDATA.48 3KB

Contincd.smp 2KB

PAM25.INP 898B

dentplus 259B

Contin.SMP 106KB

run_inp.bat 433B

CONTIN.CD 2KB

SSDATA.56 3KB

SSDATA.50 3KB

run_clst.bat 464B

slshalfa 269B

Continll.exe 420KB

summary.smp 11KB

CDDATA.29 17KB

reconCD.out 2KB

CRDATA.EXE 202KB

SELCON3.EXE 300KB

dentbeta 265B

CDSSTR.EXE 307KB

CDDATA.BB 6KB

reconCD.smp 2KB

run_cdss.bat 412B

数据处理方法.doc 345KB

FAQ.html 8KB

CDDATA.DN 3KB

SSDATA.AB 1KB

dentalfa 262B

CDPro.htm 30KB

plusalfa 266B

CDDATA.50 28KB

ReadMe.htm 14KB

CDDATA.56 31KB

CDDATA.AB 13KB

BASISPG.SMP 20KB

SSDATA.29 2KB

ListPro.htm 18KB

SSDATA.BB 715B

CDsstr.SMP 42KB

<!DOCTYPE doctype PUBLIC "-//w3c//dtd html 4.0 transitional//en"> <html> <head> <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"> <meta name="Author" content="Sreerama"> <meta name="GENERATOR" content="Mozilla/4.73 [en] (WinNT; U) [Netscape]"> <title>CDPro - Software for Analyzing Protein CD Spectra</title> </head> <body> CD Analysis Using CDPro via the Internet Browser <hr noshade="noshade" width="100%"> Frequently Asked Questions   <center> <table border="1" cellspacing="0" cellpadding="5" cols="1" width="100%" bgcolor="#ffffcc"> <tbody> <tr align="center"> <td align="left" valign="CENTER">Q: What is CDPro? A: CDPro is a suite of programs for protein CD analysis. It contains three popular CD analysis programs [CONTIN, CDSSTR, and SELCON3], a program to generate INPUT file that is used by all three programs, and a program [CLUSTER] for determining the tertiary structure class from CD spectrum. The CD analysis programs use multiple sets of reference proteins [CD and secondary structure data] and these are also provided in this site. Download the CDPro.zip file and unzip it from your C: drive. CDPro directory will be created with all necessary files. Open the RunCDPro.html file from a internet browser. (Netscape 4.7 or IE6.0). Q: How do I use CDPro? A: CDPro can be used either in a PC or on any computer. The executables and the browser-based linker for analysis are provided at this site; download CDPro.zip. The programs need to be compiled for any other computer. The INPUT file need to be generated before executing the CDPro programs. Q: What spectral range should be used for a good analysis? A: Normally, one should use CD spectra at least in the range 190-240 nm. But sometimes experimental conditions limit the range to 200 nm or so, and the flexibility of the refernce sets in the more recent programs allows the use of 200-240 nm in CD analyses. The reliability, however, is slightly reduced as one reduces the wavelength range. Comparison of performances of the two spectral ranges are available in Sreerama et al. Anal. Biochem. (2000) Q: What are units of CD data used in the analysis? A: The CD spectra should be in per residue molar absorbance units (De M-1 cm-1). Most CD instruments have the software to convert raw CD data to either molar ellipticity or molar absorbance units. Be sure to divide the CD data by the number of residues in the protein. The CD data in either molar ellipticity or molar absorbance units can be used in the CRDATA program to generate the INPUT file. Q: How do I generate the Input file? A: The analysis programs are written is FORTRAN and they require CD data in a certain format. The file "INPUT" need to be created containing the CD data, wavelength range, etc. It can be done using a program called "CRDATA" which converts CD data from any CD instrument in a text file to the required format. You will have to refer to the manual or check the software that came with your CD instrument. The text file should contain only wavelength and CD value in each line. Check the examples provided. Q: How do I choose a reference set? A: The reference set with the largest number of proteins should be chosen. This often depends on your CD data. If your CD data is only down to 190 nm or so (say, 190-250 nm) then you can select the reference set with 43 proteins (Basis_1 =  4). But if you have CD data down to 180 nm (180-250 nm) then it would be wise to use the reference set with 29 proteins, which has CD data in the range 178-260 nm. Our studies have suggested that the limitaions introduced in the analysis by the lack of short-wavelength data (180 to 190 nm) is partially overcome by the use of a larger reference set. Q: Which values can I change, and How do I change them, in the INPUT file?  A: The only values that may be changed in a properly generated INPUT file are IPRINT (from 0 to 1) and Basis_1 (any value between 1-10).Changing IPRINT to 1 would generate the output for every iteration and this should be done if a problem is suspected in the analysis; otherwise the standard output is sufficient to examine the results. Basis_1 value determines the reference set to be used in the analysis. Normally, the largest reference set available for the wavelength range should be used. Value of 8 selects a reference set based on the tertiary class determined by the CLUSTER program which should be run prior to its selection. Values 6 and 7 select reference sets with denatured CD spectra, and should be used for studying CD spectra under denaturing conditions. Consult the Readme and other help files provided. The changes in the INPUT file can be made using a text editor; Edit_Input button at the top of the screen can be used to open the DOS editor on your PC. Q: How do I read the results? A: Each program (CDSSTR, CONTINLL, and SELCON3) has a separate output (program_name.OUT) which contains results at various stages. Summary of the run (title, reference set, program and secondary structure) is added to ProtSS.OUT (execution of each of these programs write to this file). The calculated CD spectrum (corresponding to the result) is also output -- see next Q. Q: Can I compare the Calculated CD spectra with Experiment? A: Yes. The calculated CD spectrum (from each program) is compared with the experimental spectrum in files: CalcCD.OUT, reconCD.OUT and CONTIN.CD. They can be imported into a plotting software, such as Axum or SigmaPlot . The programs also calculate the RMSD between the two and print the result in program_name.out and ProtSS.out files. Q: What are RMSD and NRMSD? A: These are the RMS and normalized RMS differences between the calculated and experimental CD spectra. They can be different from different reference sets and different programs. For a given INPUT file (given CD data and a chosen reference set) both RMSD and NRMSD decrease in the order:  SELCON3 > CDSSTR > CONTINLL. This difference has to do with the algorithm and these values should not be used to judge the quality of the analysis.</td> </tr> </tbody> </table> </center>   </body> </html>