ChemDes is a free web-based platform for the calculation of molecular descriptors and fingerprints, which provides more than 3,679 molecular descriptors that are divided into 61 logical blocks.In addition, it provides 59 types of molecular fingerprint systems for drug molecules, including topological fingerprints, electro-topological state (E-state) fingerprints, MACCS keys, FP4 keys, atom pairs fingerprints, topological torsion fingerprints and Morgan/circular fingerprints, et al.
Over the past two decades, statistical machine learning methods have been successfully employed in the structural, functional and interaction profiles research of proteins and peptides. The structural and physicochemical descriptors have been intensively applied in the research of protein structure and functionalities. ProtrWeb, a web server based on our R package protr, dedicated to compute such structural and physicochemical descriptors. Currently, ProtrWeb offers twelve types of the commonly used descriptors presented in the protr package.
TargetNet is an open web server that could be used for netting or predicting the binding of multiple targets for any given molecule. TargetNet simultaneously constructs a large number of QSAR models based on current chemogenomics data to make future predictions. When the user submits a molecule, the server will predict the activity of the user’s molecule across 623 human proteins by establishing the high quality QSAR model for each human protein, thus generating a DTI profiling that can used as a feature vector for wide applications.
BioTriangle is a feature-rich toolkit used for the characterization of various complex biological molecules and interaction samples, such as chemicals, proteins, DNA/RNA, and their interactions. Biotriangle calculates nine types of features including chemical descriptors or molecular fingerprints, structural and physicochemical features of proteins and peptides from amino acid sequence, composition and physicochemical features of DNA/RNA from their primary sequences, chemical-chemical interaction features, chemical-protein interaction features, chemical-DNA/RNA interaction features, protein-protein interaction features, protein-DNA/RNA interaction features, and DNA/RNA-DNA/RNA interaction features. We recommend BioTriangle to analyze and represent various complex molecular data under investigation. We hope that the webserver will be helpful when exploring questions concerning structures, functions and interactions of various molecular data in the context of systems biology.