Missense mutations may cause different effects based on the position of mutation. If mutation occurred in the active site of an enzyme, it may lose activity/ decreased activity/  no effect on the activity depend on the mutation. This can be monitored through enzyme activity. In case of protein -protein interactions, a missence mutation may disrupt secondary structure of a protein, and disrupts protein-protein interactions. The effect can be monitored through Iso thermal calorimetry (ITC). In pymol you can mutate to desirable amino acid    by clicking wizard/mutagenesis/click on desired aminacid/change to required aminoacid.

Many Machine learning based classifiers have been developed for classifying nsSNPs into deleterious or neutral mutations. Famous ones include

PolyPhen II: "http://genetics.bwh.harvard.edu/pph2"

HANSA: "http://hansa.cdfd.org.in:8080"

SIFT: "http://sift.jcvi.org/"

Hope Server: "http://www.cmbi.ru.nl/hope/input"

I've had some good experience with the Hope Server as well.

Pymol allows you to visualise the position of a mutation as long as you have an experimental structure or model of your protein. You can then analyse whether the mutation is located in the vicinity of the active site (may affect enzymatic activity), in a protein-protein interface (may affect affinity of the interaction), in the interior of th protein (may destabilise the protein or affect its folding efficiency) or on a surface not involved in known interactions. Rosetta ddG is one program that can be used to assess the energetic consequences of a mutation, if you have a structure or reliable model of the wild type protein. Sequence based predictions look at whether the same mutation occurs naturally in a set of evolutionary related sequences. The best analysis tools combine the analysis of a 3D model with the analysis of sequence variability in the mutated position when comparing a large set of related sequences from different organisms.

If you have a solved protein structure (or homology model) you can predict effects of mutations on protein stability using mCSM or DUET:

• mCSM: http://bleoberis.bioc.cam.ac.uk/mcsm/stability
• DUET: http://bleoberis.bioc.cam.ac.uk/duet/

or in protein-protein affinity or protein-nucleic acid affinity:

• mCSM-PPI: http://bleoberis.bioc.cam.ac.uk/mcsm/protein_protein
• mCSM-NA: http://bleoberis.bioc.cam.ac.uk/mcsm/protein_dna

All aforementioned methods will quantitatively assess the mutation effects.

Dear friend for beginner and even for experts the best option in my experience is MutationTaster http://www.mutationtaster.org/

its easy simple and covers alot. 

Best of luck

Hello all, I see this is an old post but I was hoping for some advise on utilizing some of these tools to study the effect of point deletion/frameshift mutation? I tries to use SIFT/Provean but they gave me a blank output file indicating the mutation might be deleterious. I did not get any scores or any other details. I want to study how the point deletion affects the overall mRNA, i.e. stop site, splicing, mature mRNA sequence and thereby protein sequence. Please advise. Thanks!