#Pymol tutorial ucla Pc#

MODELLER then automatically calculates a model containing all non-hydrogen atoms, within minutes on a modern PC and with no user intervention. In the simplest case, the input is an alignment of a sequence to be modeled with the template structures, the atomic coordinates of the templates, and a simple script file. MODELLER is a computer program for comparative protein structure modeling ( Sali and Blundell, 1993 Fiser et al., 2000). SwissModel Workspace ( Arnold et al., 2006)īASIC PROTOCOL: MODELING LACTATE DEHYDROGENASE FROM TRICHOMONAS VAGINALIS (TvLDH) BASED ON A SINGLE TEMPLATE USING MODELLER Prosa2003 ( Sippl, 1993 Wiederstein and Sippl, 2007) MolIDE ( Wang et al., ( Song et al., 2013) Swiss-PDB Viewer ( Kaplan and Littlejohn, 2001)Ĭomparative Modeling, Threading, and Refinement T-Coffee ( Notredame et al., 2000 Notredame, 2010)Īlignment 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) 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. 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).Ĭomparative modeling consists of four main steps ( Marti-Renom et al., 2000 Fig.

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.

Functional characterization of a protein sequence is one of the most frequent problems in biology.

Pymol tutorial ucla