title: MANORAA (Mapping Analogous Nuclei Onto Residue And Affinity) for identifying protein-ligand fragment interaction, pathways and SNPs.
abstract: Protein-ligand interaction analysis is an important step of drug design and protein engineering in order to predict the binding affinity and selectivity between ligands to the target proteins. To date, there are more than 100 000 structures available in the Protein Data Bank (PDB), of which ∼30% are protein-ligand (MW below 1000 Da) complexes. We have developed the integrative web server MANORAA (Mapping Analogous Nuclei Onto Residue And Affinity) with the aim of providing a user-friendly web interface to assist structural study and design of protein-ligand interactions. In brief, the server allows the users to input the chemical fragments and present all the unique molecular interactions to the target proteins with available three-dimensional structures in the PDB. The users can also link the ligands of interest to assess possible off-target proteins, human variants and pathway information using our all-in-one integrated tools. Taken together, we envisage that the server will facilitate and improve the study of protein-ligand interactions by allowing observation and comparison of ligand interactions with multiple proteins at the same time. (http://manoraa.org).
authors.affiliation: Institute of Molecular Biosciences, Mahidol University, Salaya, Nakhon Pathom 73170, Thailand Integrative Computational BioScience (ICBS) Center, Mahidol University, Salaya, Nakhon Pathom 73170, Thailand duangrudee.tan@mahidol.ac.th.
authors.forename: Duangrudee
authors.identifier: http://orcid.org/0000-0002-9080-3303
authors.initials: D
authors.lastname: Tanramluk
authors.affiliation: Integrative Computational BioScience (ICBS) Center, Mahidol University, Salaya, Nakhon Pathom 73170, Thailand Department of Computer Engineering, Faculty of Engineering, Mahidol University, Salaya, Nakhon Pathom 73170, Thailand.
authors.forename: Lalita
authors.initials: L
authors.lastname: Narupiyakul
authors.affiliation: Integrative Computational BioScience (ICBS) Center, Mahidol University, Salaya, Nakhon Pathom 73170, Thailand Department of Computer Science, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand.
authors.forename: Ruj
authors.initials: R
authors.lastname: Akavipat
authors.affiliation: Department of Obstetrics and Gynaecology, University of Cambridge, The Rosie Hospital, Cambridge CB2 0SW, UK.
authors.forename: Sungsam
authors.initials: S
authors.lastname: Gong
authors.affiliation: Integrative Computational BioScience (ICBS) Center, Mahidol University, Salaya, Nakhon Pathom 73170, Thailand Department of Biochemistry, Faculty of Science, Mahidol University, Ratchathewi, Bangkok 10400, Thailand.
authors.forename: Varodom
authors.initials: V
authors.lastname: Charoensawan
mesh_terms: D030562:Databases, Protein; D006801:Humans; D021621:Imaging, Three-Dimensional; D020407:Internet; D008024:Ligands; D020641:Polymorphism, Single Nucleotide; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism; D012984:Software; D014584:User-Computer Interface
chemical_list: D008024:Ligands; D011506:Proteins