Biomedical subjects

Lesheng Kong

Publications and source records attributed to Lesheng Kong.

3 recordsLinked to original sources

PubMed2006

MPID-T: database for sequence-structure-function information on T-cell receptor/peptide/MHC interactions.

UNLABELLED: Normal adaptive immune responses operate under major histocompatibility complex (MHC) restriction by binding to specific, short antigenic peptides and presenting them to appropriate T-cell receptors (TcRs). Sequence-structure-function information is critical in understanding the principles governing peptide/MHC (pMHC) and TcR/pMHC recognition and binding. A new database for sequence-structure-function information on TcR/pMHC interactions, MHC-Peptide Interaction Database version T (MPID-T), is now available with the latest available Protein Data Bank (PDB) data and interaction parameters on TcR/pMHC complexes. MPID-T is a manually curated MySQL database containing experimentally determined structures of 187 pMHC complexes and 16 TcR/pMHC complexes available in the PDB. Each structure is manually verified, classified, and analysed for intermolecular interactions (i) between the MHC and its corresponding bound peptide and (ii) between TcR and its bound pMHC complex where TcR structural information is available. The MPID-T database retrieval system has precomputed interaction parameters that include solvent accessibility, hydrogen bonds, gap volume and gap index. Structural visualisation of the TcR/pMHC complex, pMHC complex, MHC or the bound peptide can be performed using freely available graphics applications such as MDL Chime or RasMol, while structural alignment (based on MHC class and peptide length) can be viewed using the Jmol molecular viewer or an MDL Chime-compatible web browser client. MPID-T contains structural descriptors for in-depth characterisation of TcR/pMHC and pMHC interactions. The ultimate purpose of MPID-T is to enhance the understanding of the binding mechanism underlying TcR/pMHC and pMHC interactions by mapping the TcR footprint on the MHC and its bound peptide, as this eventually determines T-cell recognition and binding. AVAILABILITY: The MPID-T database retrieval system is available at http://surya.bic.nus.edu.sg/mpidt CONTACT: Joo Chuan Tong (jctong@i2r.a-star.edu.sg).

Animals↗

PubMed2004

SDPMOD: an automated comparative modeling server for small disulfide-bonded proteins.

Small disulfide-bonded proteins (SDPs) are rich sources for therapeutic drugs. Designing drugs from these proteins requires three-dimensional structural information, which is only available for a subset of these proteins. SDPMOD addresses this deficit in structural information by providing a freely available automated comparative modeling service to the research community. For expert users, SDPMOD offers a manual mode that permits the selection of a desired template as well as a semi-automated mode that allows users to select the template from a suggested list. Besides the selection of templates, expert users can edit the target-template alignment, thus allowing further customization of the modeling process. Furthermore, the web service provides model stereochemical quality evaluation using PROCHECK. SDPMOD is freely accessible to academic users via the web interface at http://proline.bic.nus.edu.sg/sdpmod.

Conotoxins↗

PubMed2004

Delineation of modular proteins: domain boundary prediction from sequence information.

The delineation of domain boundaries of a given sequence in the absence of known 3D structures or detectable sequence homology to known domains benefits many areas in protein science, such as protein engineering, protein 3D structure determination and protein structure prediction. With the exponential growth of newly determined sequences, our ability to predict domain boundaries rapidly and accurately from sequence information alone is both essential and critical from the viewpoint of gene function annotation. Anyone attempting to predict domain boundaries for a single protein sequence is invariably confronted with a plethora of databases that contain boundary information available from the internet and a variety of methods for domain boundary prediction. How are these derived and how well do they work? What definition of 'domain' do they use? We will first clarify the different definitions of protein domains, and then describe the available public databases with domain boundary information. Finally, we will review existing domain boundary prediction methods and discuss their strengths and weaknesses.

Algorithms↗