# CBMDB: A Database for Accessing, Analyzing, and Mining CBM Information
## 1 Introduction  
Carbohydrate-binding modules (CBMs) are a sort of protein that can bind to carbohydrates and usually constitute large multi-module enzymes as a relatively independent module [1]. CBMs have been found to promote the association between an enzyme and a substrate, increasing the effective enzyme concentration on the polysaccharide surface, thus enhancing its enzymatic activity [2, 3, 4, 5]. This proximity effect has been demonstrated by several studies, where it is noticed that enzymes fail to hydrolyze insoluble substrates when CBMs are genetically removed [5]. In addition, CBMs have been proposed to be highly specific, to be able to recognize different polysaccharides, and to target enzyme binding to specific sites of the substrate [6, 7]. This substrate-targeting effect has been used as a tool for the elucidation of protein-carbohydrate interaction mechanisms [8]. The particular aromatic residues on the surface of CBMs, especially tryptophan and highly conserved tyrosine residues, play an important role in the binding of CBMs to ligands. The appropriate topology reflecting the structure of the substrate and the orientation of conserved residues located in the binding site of CBMs guide the effective binding and recognition of CBMs to the substrates [9]. Moreover, some studies have shown that the binding of CBMs to a crystalline substrate leads to the disruption of polysaccharide structures and, therefore, enhances substrate availability for enzymatic hydrolysis [10, 11]. With the development of enzyme engineering, it is important to explore more potential CBMs to elucidate the mechanism of protein-carbohydrate recognition and to promote its application in enzyme molecular modification and drug development. To date, an increasing number of CBMs have been identified and characterized. The total number of CBM entries is 277,412, which come from 88 families, and at least one 3D structure has been reported for 408 modules [9]. All of this information can be found in some comprehensive databases, such as NCBI ([[https://www.ncbi.nlm.nih.gov/](https://www.ncbi.nlm.nih.gov/)]([https://www.ncbi.nlm.nih.gov/](https://www.ncbi.nlm.nih.gov/))), PFAM ([[http://pfam.xfam.org/](http://pfam.xfam.org/)]([http://pfam.xfam.org/](http://pfam.xfam.org/))), PDB ([[https://www.rcsb.org/](https://www.rcsb.org/)]([https://www.rcsb.org/](https://www.rcsb.org/))), CAZY ([[http://www.cazy.org/](http://www.cazy.org/)]([http://www.cazy.org/](http://www.cazy.org/))), and PubMed ([[https://pubmed.ncbi.nlm.nih.gov/](https://pubmed.ncbi.nlm.nih.gov/)]([https://pubmed.ncbi.nlm.nih.gov/](https://pubmed.ncbi.nlm.nih.gov/))). NCBI's Protein Data Bank mainlyrecords the amino acid sequences of CBMs contained in relative enzymes. PFAM provides information on protein families. The 3D structure of CBMs, together with relative enzymes, can be found in PDB records. CAZy provides the GenBank accession number of CBMs. Related literature about CBMs can be searched for on PubMed. With the rapid development of high-throughput sequencing technology, a large amount of potential CBMs need to be identified, which presents a challenge for the collection, integration, and analysis of huge amounts of information. However, none of the current databases provide independent information about CBMs, and the information on CBMs is not consolidated. Furthermore, some analytical tools for CBM research, such as BLAST, Clustal Omega, structure searches, and viewing tools, are limited in these databases. All of these problems make CBM work time-consuming. To facilitate the search for and analysis of CBM information, a simple, user-friendly, and comprehensive CBM database (CBMDB) that integrates multidimensional information and analytical tools was constructed. All of the CBM data were collected and downloaded from various public sources, such as NCBI, PFAM, PDB, CAZy, and PubMed, based on indexes and API fetches. Some classic sequence and structure analysis tools, such as BLAST, Clustal Omega, and Jmol, were integrated into CBMDB.