ProCaff IITM

CarbDisMut

Carbohydrate binding proteins Disease Mutations


Glossary

Entry ID Unique identifier for the entry.
Gene Name Name of the gene that code for the protein sequence
UniProt UniProtKB accession number of the protein sequence
Mutation Protein level mutation. Eg. TRP(W) -> ALA(A)
PDB ID Protein 3D-structure ID from Protein Data Bank
Mutation type Different types of mutations Eg. Insertion, Deletion, Missense and Nonsense
Effect of mutation A given mutation is disease-associated or neutral
Disease: Mutation reported as disease-associated
Neutral: Mutation that doesn't implicated in disease
Experimental 3D structures Whether experimental 3D structure is known or not
Disease Name: Name of the disease or the disease sample (in the case of cancer) in which muations have been found
Disease class 14 different classes based on Kegg Human disease
Source Name of the data source 1. Humsavar 2. SwissVar 3. ClinVar 4. COSMIC 5. 1000 Genomes
Conservation Score The residues are evolutionary important. Score varies between 0 (very less conserved) and 1 (more conserved)
Results per page Users can select number of result entries in per page. Maximum upto 200.
Search by Conditional operator to search the user queries
Chromosome number and genome position Mutation at genomic position on a chromosome
Nucleotide mutation Gene level mutation (Eg. TCC -> TGC)
Origin Origin of the mutation whether it is Germline, Somatic or unknown
Germline: mutation occurs in a germ cell
Somatic: mutation occurs in a somatic cell
Unknown: origin unknown
Interface residues Whether the mutation site is located in the interface of protein-carbohydrate complexes or not
Predicted ΔΔG residues Predicted ΔΔG (kcal/mol) values using our earlier prediction method based on protein-carbohydrate classifications (PCA-MutPred).
Neighbouring residues The neighboring residues of the mutation site on both N and C terminals using window length 7
PDB residues mapped Mutation is mapped with 3D structure numbering for each PDB ID and chain (if available)
Uniprot Isoforms UniprotKB accession number of the isoform in the case where the mutation matches to the isoform sequence
Glycosciences.de Information about the carbohydrate structures
(i) pdb2linucs (Carbohydrate information in LINUCS-Code)
(ii) pdb-care (PDB CArbohydrate REsidue check)
(iii) CARP (CArbohydrate Ramachandran Plot)
Glygen Computational and Informatics Resources for Glycoscience
GlyTouCan Unique accession numbers to glycan from GlyTouCan repository

CarbDisMut

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Protein Bioinformatics Lab,
Department of Biotechnology,
Indian Institute of Technology Madras.

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