MODELLER @ BioHPC

MODELLER is used for homology or comparative modeling of protein three-dimensional structures. The user provides an alignment of the sequence to be modeled (i.e., the TARGET) and the sequence(s) of known structure(s) [i.e., the TEMPLATE(S)]. The program automatically generates a model containing all non-hydrogen atoms. MODELLER implements comparative protein structure modeling by satisfaction of spatial restraints. While our current implementation performs only this task, the "full version" of MODELLER can be used in many other applications, including de novo modeling of loops in protein structures, optimization of various models of protein structure with respect to a flexibly defined objective function, multiple alignment of protein sequences and/or structures, clustering, searching of sequence databases, comparison of protein structures, etc. For more information please go to MODELLER home page. In our site, MODELLER (version 9v3) runs on the Real-Time cluster.

Job name: (please, no spaces, special characters etc., uderscore is OK)

ALIGNMENT FILE:

PIR format ; MODELLER format ; BLAST format .

File with alignment(s):

Warning: If you are using more than one template, the multiple-alignment file you upload must include: (a) an aligned sequence for every template you add, and (b) a single copy of you target sequence.

TARGET (or QUERY) SEQUENCE:

Target Sequence Name in Alignment File:

TEMPLATE STRUCTURE(S):

Download pdb from

SECONDARY-STRUCTURE RESTRAINTS (Optional):

NUMBER OF MODELS REQUESTED:

Cluster: ( Show timeout info )