PYMOL TUTORIAL UCLA HOW TO
PYMOL TUTORIAL UCLA SOFTWARE

MolIDE ( Wang et al., ( Song et al., 2013) Swiss-PDB Viewer ( Kaplan and Littlejohn, 2001)Р”В¬omparative Modeling, Threading and Refinement T-Coffee ( Notredame et al., 2000 Notredame, 2010)Р”Р„lignment modules in molecular graphics programs GENTHREADER ( Jones, 1999 McGuffin and Jones, 2003) Sequence and structure based sequence alignment SwissModel Repository ( Kiefer et al., 2009) Protein Model Portal ( Arnold et al., 2009 Haas et al., 2013) Protein Information Resource ( Huang et al., 2007) Comparative modeling predicts the 3-D structure of a given protein sequence (target) based primarily on its alignment to one or more proteins of known structure (templates).Р”В¬omparative modeling consists of four main steps ( Marti-Renom et al., 2000 Figure 5.6.1): (i) fold assignment, which identifies similarity between the target and at least one known template structure (ii) alignment of the target sequence and the template(s) (iii) building a model based on the alignment with the chosen template(s) and (iv) predicting model errors. In the absence of an experimentally determined structure, comparative or homology modeling often provides a useful 3-D model for a protein that is related to at least one known protein structure ( Marti-Renom et al., 2000 Fiser, 2004 Misura and Baker, 2005 Petrey and Honig, 2005 Misura et al., 2006). This task is usually facilitated by an accurate three-dimensional (3-D) structure of the studied protein.

PYMOL TUTORIAL UCLA SOFTWARE

The download and installation of the MODELLER software is also described.Р”Р‡unctional characterization of a protein sequence is one of the most frequent problems in biology. Modeling lactate dehydrogenase from Trichomonas vaginalis (TvLDH) is described as an example.

PYMOL TUTORIAL UCLA HOW TO

This unit describes how to calculate comparative models using the program MODELLER and discusses all four steps of comparative modeling, frequently observed errors, and some applications. The prediction process consists of fold assignment, target-template alignment, model building, and model evaluation.

Comparative modeling predicts the 3-D structure of a given protein sequence (target) based primarily on its alignment to one or more proteins of known structure (templates). In the absence of an experimentally determined structure, comparative or homology modeling can sometimes provide a useful 3-D model for a protein that is related to at least one known protein structure. This task is usually facilitated by accurate three-dimensional (3-D) structure of the studied protein. Functional characterization of a protein sequence is one of the most frequent problems in biology.

Pymol tutorial ucla