Another potential area for applying the molego approach is in homology modeling.

Consequently, they often cannot be modeled using standard homology modeling techniques.

The critical first step in homology modeling is the identification of the best template structure, if indeed any are available.

That also explains why protein threading may be more effective than homology modeling in many cases.

The usual four steps of homology modeling are executed:

Several large-scale benchmarking efforts have been made to assess the relative quality of various current homology modeling methods.

In homology modeling, a common application of fragment libraries is to model the loops of the structure.

If a sequence has no significant homology found, homology modeling may not give reliable prediction in this case.

The accuracy of the structures generated by homology modeling is highly dependent on the sequence identity between target and template.

Homology modeling is a computational method to build tertiary structures from amino-acid sequences.

ESyPred3D is an automated homology modeling program.

Determining the structure a novel protein allows homology modeling to more accurately predict the fold of other proteins in the same structural family.

Key words: molecular dynamics simulation, ABC transporters, homology modeling.

Key words: actin-binding proteins, homology modeling, chemical cross linking, actin-severing proteins.

The deficiencies of the interatomic potentials remain a major bottleneck in homology modeling of proteins.

Domains with structural homologs then follow a "template-based model" (i.e., homology modeling) protocol.

Protein threading is more effective than homology modeling, especially for proteins which have few homologs detectable by sequence alignment.

MethylGene: Homology modeling and ligand docking for an enzyme implicated in cancer proliferation.

The results of e.g. in silico mutations or homology modeling with FoldX can be directly analyzed on screen.

Homology modeling is currently the most accurate method to generate reliable three-dimensional protein structure models and is routinely used in many practical applications.

The method of homology modeling is based on the observation that protein tertiary structure is better conserved than amino acid sequence.

The homology modeling procedure can be broken down into four sequential steps: template selection, target-template alignment, model construction, and model assessment.

Homology modeling and protein threading are both template-based methods and there is no rigorous boundary between them in terms of prediction techniques.

In other words, homology modeling is for "easier" targets and protein threading is for "harder" targets.

Homology modeling treats the template in an alignment as a sequence, and only sequence homology is used for prediction.

The three-dimensional structure of a flavonol O-methyltransferase was studied through homology-based modeling, using a caffeic acid O-methyltransferase as a template, to explain their strict substrate preferences.

One strength of having a consortium of modelers is the ability to employ a comparative modeling approach.

A structural model of DS151 was obtained by comparative modeling studies with segment 1 of gelsolin.

Tertiary structure can be predicted from the sequence, or by comparative modeling (when the structure of a homologous sequence is known).

MODELLER is used for homology or comparative modeling of protein three-dimensional structures (1).

The Robetta server is an automated protein structure prediction service offered by the Baker laboratory for non-commercial ab initio and comparative modeling.

He published his findings in a paper "The Clash of Peoples in Civilizations with the Comparative Modeling Perspective."

The 'Template based modeling' category includes all former comparative modeling, homologous fold based models and some analogous fold based models.

Models are created by the comparative modeling pipeline ModPipe which relies on the MODELLER program.

Many also enable the alignment to be edited to correct these (usually minor) errors, in order to obtain an optimal 'curated' alignment suitable for use in phylogenetic analysis or comparative modeling.

The researchers, part of the Cancer Intervention and Surveillance Modeling Network, utilized a comparative modeling approach in which they constructed detailed cigarette smoking histories for individuals born from 1890 through 1970.

Homology modeling, also known as comparative modeling of protein, refers to constructing an atomic-resolution model of the "target" protein from its amino acid sequence and an experimental three-dimensional structure of a related homologous protein (the "template").

These include Proteus2 to perform structural modeling, PREDITOR to calculate torsion angles from chemical shifts, PPT-DB for comparative modeling and alignment and CS23D to calculate protein structures from chemical shifts only.