nest is a program for homology modeling.

Download software

Click here to download nest.

System requirements

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.

Using nest

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.