homology modeling (Animalia)

Knowledge graph centered on homology modeling (Animalia) with 29 nodes and 105 connections. Top connected: Pekania pennanti, Lepidoptera, Diptera, Bacteria, Arabidopsis thaliana.

Method synopsis

Three-dimensional protein structure prediction using homology modeling to assess the structural impacts of amino acid polymorphisms on PEPCK protein structure and bonding interactions.

Synthesized from method descriptions across 1 paper using this protocol.

Procedure from a recent peer-reviewed implementation

Steps below were extracted from the most recent peer-reviewed implementation of this protocol in the corpus — A genetic polymorphism evolving in parallel in two cell compartments and in two clades (2013), BMC Evolutionary Biology. Implementations in other papers (listed below) may differ.

1. Structural modeling
   Performed homology-based structural modeling using 3D-Jury metaserver and MODELLER 9.8. Generated 5 replicates for each model and selected best-scoring model using lowest molpdf criterion. Visualized models and measured structural features using DeepView (Swiss-PDB Viewer) 4.0.1. Template structures were obtained from Protein Data Bank.
   Quantities: 5 replicates per model, best-scoring model selectedDuration: Not specifiedConditions: Computational structural analysis
   Equipment: 3D-Jury metaserver, MODELLER 9.8, DeepView (Swiss-PDB Viewer) 4.0.1, Protein Data Bank

Typical Equipment

• 3D-Jury metaserver
• MODELLER 9.8
• DeepView (Swiss-PDB Viewer) 4.0.1
• Protein Data Bank

Output Measurements

• 3D protein structures
• structural features
• bonding patterns

Papers Using This Protocol (1)

Species Studied With This Protocol

Places Where Used