The protein-protein docking problem is one of the focal points of activity in computational biophysics and structural biology. The three-dimensional structure of a protein-protein complex, generally, is more difficult to determine experimentally than the structure of an individual protein. Adequate computational techniques to model protein interactions are important because of the growing number of known protein structures with experimental methods or with computational methods like homology protein models, particularly in the context of structural genomics.

Our Molecular Docking Services uses tools for fundamental studies of protein-protein docking interactions and provide a structural base for drug designing. Protein-protein docking is the prediction of the structure of the complex, given the structures of the individual proteins. Designing the standard protocol for molecular docking approaches, we at RASA deal with studies related to the conformational changes between unbound and bound structures, as well as the inaccuracies of the interacting modelled structures, often in a high-throughput mode needed for protein modeling of large networks of protein-protein interactions. Our Molecular Docking Services is developed in an adequate docking manner which is facilitated by rapidly expanding information and data resources, growing computational capabilities, and a deeper understanding of the fundamental principles of protein-protein interactions.

The interactions between protein and nucleic acids play essential roles in various essential biological processes, including DNA replication, RNA transcription, RNA splicing, degradation of nucleic acids and protein synthesis. Defects in protein–nucleic acid interactions are implicated in a number of diseases, ranging from neurological disorders to cancer. However, experimental determination of most protein–nucleic acid complex structures by high-resolution methods is a tedious and difficult process.

Computational techniques complement experimental approaches in elucidating protein–nucleic acid interactions. Our in-silico molecular docking services studies docking of proteins with nucleic acids, by building theoretical models of the complex structures at atomic details, can yield sufficient information to build a working hypothesis and guide further experimental analyses to identify important amino acids or nucleotide residues. This is an important means for understanding the physicochemical forces that underlie macromolecular interactions and a valuable tool for modelling protein–nucleic acid complex structures at the atomic level. Furthermore, the precise understanding of these interactions involving disease-implicated targets is ever more critical for the rational design of biologic-based therapies.

We at RASA makes use of several software tools for Molecular Docking Services. The general procedure involves a rigid body global search and geometrically plausible protein–nucleic acid complex structures are generated, user-defined restraints can be applied to limit the search space. As per our molecular docking services’ protocol, the resulting models are scored and ranked using statistical potentials, developed specifically for protein–RNA or protein–DNA complexes. The best-scored structures are then clustered and representatives of the largest clusters are then selected for structural optimization via energy minimization before being presented in the final report for the respective service.

Computational docking study is widely used for study of protein-ligand interactions and for drug discovery and development. It can be used to predict bound conformations and free energies of binding for  ligands to molecular targets. Docking study is used particularly for the study of bio-molecular interactions and mechanisms, and is applied to structure-based drug design. The methods are fast enough to allow virtual screening of ligand libraries containing tens of thousands of compounds. Typically the process starts with a target of known structure, such as a crystallographic structure of an enzyme of medicinal interest. Docking study  is then used to predict the bound conformation and binding free energy of small molecules to the target. Single docking experiments are useful for exploring the function of the target, and virtual screening, where a large library of compounds are docked and ranked, may be used to identify new inhibitors for drug development. We at RASA follow a protocol for Molecular Docking Services which covers the docking and virtual screening methods including a basic docking of a drug molecule with a particular target- for example an anticancer target, a virtual screen of this target with a large ligand library, docking with selective receptor flexibility, active site prediction or pocket of protein, and docking with explicit hydration.