nest is a program for homology modeling.
The current version of nest supports the following platforms: SGI and Intel Linux.
nest is a program for modeling protein structure based on a given sequence-template alignment. It has the following capabilities:
- model building with artificial evolution
- sequence alignment tuning
- composite structure building
- model building based on multiple templates
- structure refinement
nest can be used to build homology models based on:
- a single sequence-template alignment
- from multiple templates for the entire structure
- from different templates used for different regions of the structure
It also carries out energy based structure refinement and can change an alignment based on energetic considerations.
Usage: nest -seed num -fast num-tune num -log str -opt num -nopt num-out num file.pir
-fast fast mode.from 0-5; default is 3.with 5 fastest
-tune alignment tuning, from 0-3; defautl is 0.
0,no alignment tuning
1,remove gaps in secondary strucutre
2,remove zig-zag gapsplus -tune 1;
3,remove terminal gaps plus -tune 2;
-opt refine mode, from 0-4; default is 1.with 4 thorough refinement
0, no minimization at all;
1, remove atom clashes;
2, refine in insertion and deletion regions, usually loop regions;
3, refine in all loop regions;
4, refine in all loop and secondary regions
-out output mode, from 0-2, defautl is 0. with 2 all intermediate output
0, only final structures written down;
1, intermediate structures also outputted;
2, more intermediate output
-seed set seed number, defautl is 18120.
-nopt number of rounds of refinement.default is 1.
-log log file.default is standard screen output
file.pir pir alignment file
Petrey D, Xiang Z, Tang CL, Xie L, Gimpelev M, Mitros T, Soto CS, Goldsmith-Fischman S, Kernytsky A, Schlessinger A, Koh IY, Alexov E, Honig B. Using multiple structure alignments, fast model building, and energetic analysis in fold recognition and homology modeling. Proteins. 2003;53 Suppl 6:430-5.