Chem-Knowledge for Chemists and Medicinal Chemists

LSKB Database provides annotation information about genes, proteins, compounds, and their structures and literature information, which were gathered, cleaned, and organized from over 20 public databases related to genomes, compounds, diseases, and organs. In particular, over 40 million compounds are categorized with annotations based on their structures and have been processed to remove as many repetitions as possible.

LSKB Chem Knowledge applies various search functions for data retrieved from compound databases. It includes compound information, structures, BioAssay, and PDB complex Ligand information. This system makes it possible to obtain a variety of functional information via keyword and chemical structure searches. It also provides functions to perform a literature search from the chemical structure even if we do not know its function, and searches for binding proteins and highly active proteins.
LSKB always provides you the information of the chemicals together with genes, protein, or diseases, etc. by literature entries.

LSKB always provides you the information of the chemicals together with genes, protein, or diseases, etc. by literature entries.

Chem-Knowledge can use several purpose

BioAssay

For establishing your assay, the review and evaluation system is important. There are well validated and tested results available in public databases. LSKB was designed to support establishing an assay using such information.

HTS

In an analysis of Hit compounds of HTS, a clustering of compounds based on their structures is effective. LSKB will quickly obtain information about the types of functions of compound clusters (e.g. related proteins and diseases) from results of literature mining. Furthermore, a search for available compounds can be conducted using the LSKB Zinc database.

FBDD

When a target protein is well-defined, in silico screening or FBDD is an effective method. By listing the data registered in the PDB database regarding the target protein, it is possible to verify ligands and active sites. Also the examination of similarity searches of Hit fragments and profiling of compounds having Hit fragments as partial structures can be conducted by observing and analyzing fragment-bound composite structures.

In-silico screening

Using LSKB, it is possible to survey structurally important information (e.g. interactions between proteins and ligands) based on the PDB information and composite structures of target proteins.
Furthermore, narrowing and filtering functions are possible during the structural search for similar structures or partial structural similarity of bound ligands.

Library Design

In the library design, not only structures of known active compounds or target binding ligands can be used as queries for similar structures and partial match searches but also structures based on the idea of researchers. This allows for the usage of LSKB to construct a library using commercially available compounds and to validate the novelty of the designed library.

Structure analysis

In the case of lead search and optimization, LSKB conducts a structure modification of a ligand using internal data or structural information of composites from the PDB database. Furthermore, it offers the possibility to search for similar compounds and partial structures with interesting scaffolds from public structural databases.