The folder contains a list of programs to compute normalized interface packing (NIP) and normalized surface complementarity (NSc) score. Developed by Pralay Mitra at Indian Institute of Science, Bangalore. Copyright (C) 2010-2015 Pralay Mitra If you are using this software then please cite: Mitra, P. and Pal, D. (2010). New measures for estimating surface complementarity and packing at protein-protein interfaces. FEBS Lett. 584(6):1163-1168. If you have any difficulty in running the executables please feel free to contact - ------------------------------------------------- | Pralay Mitra, Ph.D. | | c/o Dr. Debnath Pal | | Bioinformatics Center | | Department of Computational and Data Sciences | | Indian Institute of Science | | Bangalore - 560012, India | | Email: pralay@cse.iitkgp.ernet.in | ------------------------------------------------- ======================================================================================================================== ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ======================================================================================================================== HOW TO ======================================================================================================================== ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ======================================================================================================================== The folder contains a README file, and three binary executable files compiled in X86 architecture. Binary file (nip_nsc_32bitLinux.exe) has been compiled using GCC 4.1.1 under 32 bit Fedora Core 5 environment (Intel), binary file (nip_nsc_64bitLinux.exe) is compiled using GCC 4.3.2 under 64 bit Fedora Core 10 (AMD) and binary file (nip_nsc_32bitMacDarwin.exe) is compiled in Macintosh OS under Darwin linux (Kernel Version 10.4.0) in i386 architechture. In all cases -static option has been used to statically link the libraries. DEPENDENCIES: nip_nsc uses NACCESS software for computing interface area and takes the path of naccess program as second argument. Please download and install the freely available NACCESS program from: http://www.bioinf.manchester.ac.uk/naccess/. There are system specific binary files. Each file name is suffixed with system architechture. Please download according to your system architecture. USAGE: ./nip_nsc IMPORTANT POINTS: THE SOFTWARE SUPPORTS PDB FORMAT FILES ONLY. This version of the program takes ONLY ATOM coordinates (non Hydrogen atoms) from the PDB file. The program is developed for working on only one interface per protein complex at a time. Therefore please make sure that there is only one interface in your input PDB file. Please also ensure that in your PDB file only one entry is there for atoms with occupancy less than 1.0. If you have more than one entry for atoms with occupancy less than 1.0, the program will skip all entries for that atom. ======================================================================================================================== ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ======================================================================================================================== KNOWN ISSUES ======================================================================================================================== ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ======================================================================================================================== 1. In some systems a newline is required at the end of pdblist file (terminated by a newline). ======================================================================================================================== ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ======================================================================================================================== EXAMPLE RUN ======================================================================================================================== ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ======================================================================================================================== 1. If your system is 32 bit linux system, then download nip_nsc_32bitLinux.exe and keep in a folder (say, /home/user/nip_nsc/). Grant execute permission to this file: chmod a+x nip_nsc_32bitLinux.exe 2. Download example PDB file pdb12as.ent and put in some folder (say /home/user/pdb/). 3. In folder /home/user/nip_nsc/ create one file with name pdblist and include the name of the complex you want to work with. For example:pdb12as.ent. If you want to run on several proteins then you have to mention name of all the protein complexes in this file (one name per line). 4. Download and install NACCESS program (from http://www.bioinf.manchester.ac.uk/naccess/) in some folder. Say the name of the folder is /home/user/naccess/ 5. Now, execute the binary file nip_nsc_32bitLinux.exe in folder /home/user/nip_nsc/ using command: ./nip_nsc_32bitLinux.exe /home/user/pdb/ /home/user/naccess/ 6. Time requirement is few seconds per protein complex. 7. The program will write a number of temporary files during execution which will be removed after successful completion of the program. 8. Finally, one output file will be in the folder /home/user/nip_nsc/ viz, NIP_NSc_score.txt. If any file with this name is already present in the folder, it will be over written. 9. Corresponding to each protein there will be one row. Each row contains 4 TAB delimited columns. PDBfilename, InterfaceArea, NIP and NSc scores.