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2.0
3D Server
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Sequence based analysis
(Please provide a nucleotide sequence as input and submit the job)
Paste nucleotide sequence below
Paste raw nucleotide sequence or in fasta, GCG or Genbank format
Or upload sequence file
Upload the file of raw nucleotide sequence or in fasta, GCG or Genbank format
example file
Define mutagenesis method*
MAP analysis performed upon 19 commonly used random mutagenesis methods. Please click here to include another mutagenesis method in MAP analysis.
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Transition: A -> G
8.33
T -> C
8.33
G -> A
8.33
C -> T
8.33
Transversion: A -> T
8.33
T -> A
8.33
A -> C
8.33
T -> G
8.33
Transversion:
G -> C
8.33
C -> G
8.33
G -> T
8.33
C -> A
8.33
*Please mouse over the input labels for help!
Processing... Do not refresh the page!
Processing... Do not refresh the page!
Structure based analysis
(Please provide the PDB file along with the nucleotide sequence as input and submit the job)
Upload PDB file
Upload the crystallographic structure or homology model of the protein (Identity should be more than 80% for the best results)
example PDB
Chain
Please enter the chain id in case of multimer structure
A
Select method
Please select one random mutagenesis method from the dropdown menu
Non biased
Taq(-, G>A=C=T)
Taq(+, G=A=C=T)
Taq(+, G>A=C=T)
Taq(+, G>>A=C=T)
Taq(+, G=A, C=T)
Taq(+, G=T, A=C)
Taq(I164K)
Mutazyme I
Mutazyme II
Pfu(exo-, D473G)
Transcriptase
Taq(dPTP/8-oxodGTP)
epRCA
Pol I
E. coli (mutA)
Nitrous acid
Formic acid
Hydrazine
EMS
User defined
(*Default is Non biased)
Select the amino acid group
Please select one of the amino acid group (categorized according to their chemical properties)
*Please select 'amino acid list' option to perform analysis upon a set of amino acids
All
Charged
Aromatic
Aliphatic
Neutral
Buried
Exposed
Amino acid list
(*Default is for all residues)
Enter Amino acid numbers
Enter space separated amino acid numbers in case of aminoacid list group
*By using the cutoff option the residues within the diameter of given residues can be included in the result.
Cutoff (Å)
*Please enter cutoff for the residues within the diameter of given residues.
0
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Define molecular interaction parameters*
To change the default parameters for calculation of molecular interaction
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Salt bridge (Å)
4.0
Hydrophobic interaction (Å)
5.0
Side chain hydrogen bond (Å)
3.5
Aromatic interaction (Å)
7.0
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*Please mouse over the input labels for help! **Please don't refresh the page, the query will take a while to be completed for large proteins!
Reference: Verma R, Schwaneberg U, Roccatano D 2012. MAP
2.0
3D: A sequence/structure based server for protein engineering
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