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Is there a known structure?

Enter the PDB ID:  
Each structure in the PDB is represented by a 4 character alphanumeric identifier, assigned upon its deposition. For example, 1bxl and 1d66 are identification codes for PDB entries for Bcl-Xl / Bak complex and Gal4 (Residues 1 - 65) complex with 19mer DNA, respectively.

Upload your own PDB file:  
The ATOM record is essential for ConSurf run. In case you wish to upload your own PDB file, the ATOM record must be included in it.

Do you have a Multiple Sequence Alignment (MSA) to upload? (If not, ConSurf will make an MSA for you.)

Upload your Multiple Sequece Alignment file:  
ConSurf accepts external MSAs in the 7 formats supported by CLUSTAL W. These are: NBRF/PIR, EMBL/SwissProt, Pearson (Fasta), GDE, Clustal, GCG/MSF and RSF format.
In case you provide an external MSA file in Fasta format, please use the "-" sign as the only gap symbol, as this is the only standard gap sign that ConSurf accepts.

Indicate the Query Sequence Name:  
This should be the exact name of the sequence in the provided MSA file, that corresponds to the query protein.
Paste here the protein sequence in FASTA format:

Choose parameters to homolog search algorithm

Homolog search algorithm

Nucleotides Database

BLAST E-value Cutoff

Select homologs for ConSurf analyses:

Do you have a Tree file to upload?

Upload your TREE file (in Newick format):   
In case you provide an external multiple sequence alignment (MSA) file, ConSurf can also accept a corresponding external phylogenetic tree in Newick (Phylip) format, for example: Tree File.
The names of the proteins sequences in the tree file must be identical to the names in the MSA file.

Calculation Method
The calculation method for the rate of evolution at each site in the MSA.
The Bayesian method was shown to significantly improve the accuracy of conservation scores estimations over the Maximum Likelihood method, in particular when a small number of sequences are used for the calculations. An additional advantage of the Bayesian method is that a confidence interval is assigned to each of the inferred evolutionary conservation score.

Evolutionary Substitution Model

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