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Analyze Nucleotides or Amino Acids?

Is there a known protein 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.

Chain Identifier:
 (case sensitive ie A not equal a) 

To predict 3D structure for the query protein using MODELLER, please provide MODELER license key
ConSurf offer a 3D model predicted by HHPred and MODELLER for protein-query sequence.
To use MODELLER a user required for MODELLER-key; To obtain a MODELLER-key please contact the Sali lab.
The key is freely available for academic users, and is provided automatically, without manual intervention, for users who are identifiable as such.


Do you have a Multiple Sequence Alignment (MSA) to upload?

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.

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.

Paste here the nucleotides sequence in FASTA format:

Choose parameters to build the Multiple Sequence Alignment (MSA)

Alignment program

Nucleotides Database

Maximum Homologs to collect
The maximum number of homologs, from those found by PSI-BLAST (with the given E-value), to be included in the calculation. In order to include all the homologs, replace the default value with the word "all".

Maximal %ID Between Sequences
Filter out redundant sequences. Sequences are clustered according to the given sequence identity cutoff, one representative of each cluster is reserved.

Minimal %ID For Homologs
Minimal sequence identity with the query sequence. Blast hits that shares less than the given identity cutoff are ignored

BLAST E-value Cutoff

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

Job Title


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