title: MollDE: a homology modeling framework you can click with.
abstract: Molecular Integrated Development Environment (MolIDE) is an integrated application designed to provide homology modeling tools and protocols under a uniform, user-friendly graphical interface. Its main purpose is to combine the most frequent modeling steps in a semi-automatic, interactive way, guiding the user from the target protein sequence to the final three-dimensional protein structure. The typical basic homology modeling process is composed of building sequence profiles of the target sequence family, secondary structure prediction, sequence alignment with PDB structures, assisted alignment editing, side-chain prediction and loop building. All of these steps are available through a graphical user interface. MolIDE's user-friendly and streamlined interactive modeling protocol allows the user to focus on the important modeling questions, hiding from the user the raw data generation and conversion steps. MolIDE was designed from the ground up as an open-source, cross-platform, extensible framework. This allows developers to integrate additional third-party programs to MolIDE.
  
  
  BACKGROUND
  http://dunbrack.fccc.edu/molide/molide.php
  
  
  BACKGROUND
  rl_dunbrack@fccc.edu.
authors.affiliation: Institute for Cancer Research, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA.
authors.forename: Adrian A
authors.initials: AA
authors.lastname: Canutescu
authors.forename: Roland L
authors.initials: RL
authors.lastname: Dunbrack
mesh_terms: D000465:Algorithms; D003196:Computer Graphics; D003198:Computer Simulation; D008958:Models, Molecular; D011487:Protein Conformation; D011506:Proteins / Q000032:analysis / Q000737:chemistry*; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D017386:Sequence Homology, Amino Acid; D012984:Software; D018511:Systems Integration; D014584:User-Computer Interface
chemical_list: D011506:Proteins