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.

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.

SwissProt - a curated protein sequence database which strives to provide a high level of annotation.
UniRef90 - this database clusters sequences and sub-fragments with 11 or more residues that have at least 90% sequence identity with each other (from any organism) into a single UniRef entry, displaying the sequence of a representative.
UniProt is the universal protein resource, a central repository of protein data created by combining Swiss-Prot, TrEMBL and PIR.
Clean Uniprot is a modified version of the UniProt database aimed to gather the more reliable sequenceses. See details here.
NR this database is maintained by the NCBI and comprised of non-redundant sequences from GenBank CDS translations, PDB, SwissProt, PIR, and PRF, excluding environmental samples from WGS projects.

Select homologs for ConSurf analyses:

Select sequences

closest that sample the list of homologues to reference sequence

Maximal %ID between sequences

 

Minimal %ID for homologs

 

Alignment method

MAFFT-L-INS-i PRANK MUSCLE CLUSTALW

Upload your TREE file (in Newick format):   

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.