What is ConSurf analysis?
What is ConSurf analysis?
INTRODUCTION. ConSurf is a widely used tool for revealing functional regions in macromolecules by analysing the evolutionary dynamics of amino/nucleic acids substitutions among homologous sequences (1–4).
What is ConSurf used for?
The ConSurf server (Glaser et al., 2003; Landau et al., 2005; Ashkenazy et al., 2010; Celniker et al., 2013; Ashkenazy et al., 2016) is a bioinformatics tool for estimating the evolutionary conservation of amino/nucleic acid positions in a protein/DNA/RNA molecule based on the phylogenetic relations between homologous …
How do you cite Provean?
If you publish research that uses provean you have to cite it as follows: Choi Y, Chan AP (2015) PROVEAN web server: a tool to predict the functional effect of amino acid substitutions and indels. Bioinformatics 31(16): 2745-2747.
What is a phyloP score?
phyloP scores measure evolutionary conservation at individual alignment sites. Interpretations of the scores are compared to the evolution that is expected under neutral drift. Positive scores — Measure conservation, which is slower evolution than expected, at sites that are predicted to be conserved.
What are chains in PDB?
Large proteins are composed of several discrete regions, known as chains, and this is reflected in PDB files. There are two chains in 2hac. pdb: “chain A” and “chain B”. Each amino acid in a chain is called a residue, and they are numbered sequentially.
What is Provean score?
PROVEAN Score. PROVEAN was developed to predict whether a protein sequence variation affects protein function. PROVEAN is able to provide predictions for any type of protein sequence variations including the following. Single or multiple amino acid substitutions. Single or multiple amino acid insertions.
For what research purpose can you use Provean protein software tool?
PROVEAN (Protein Variation Effect Analyzer) is a software tool which predicts whether an amino acid substitution or indel has an impact on the biological function of a protein. PROVEAN is useful for filtering sequence variants to identify nonsynonymous or indel variants that are predicted to be functionally important.
How do you interpret phyloP scores?
- Positive scores — Measure conservation, which is slower evolution than expected, at sites that are predicted to be conserved.
- Negative scores — Measure acceleration, which is faster evolution than expected, at sites that are predicted to be fast-evolving.
What does PhastCons score mean?
The PhastCons score is a probability that each nucleotide belongs to a conserved element, whereas abs(phyloP) is the -log(p-value) under a null hypothesis of neutral evolution, and a negative sign indicates faster-than expected evolution, while positive values imply conservation.