The representation of protein flexibility is still a challenge for the state-of-the-art flexible ligand docking protocols. In this article, we use a large and diverse benchmark to prove that is possible to improve consistently the cross-docking performance against a single receptor conformation, using an equilibrium ensemble of binding site conformers. The benchmark contained 28 proteins, and o...

2D-IR exchange spectroscopy has been introduced recently to map chemical exchange networks in equilibrium with subpicosecond time resolution. Here, we demonstrate the generalization of 2D-IR exchange spectroscopy to nonequilibrium systems and its application to map light-triggered migration of ligands between different sites in a protein. Within picoseconds after a photodissociating laser pulse...

This paper describes work conducted as a joint collaboration between the Virtual Design Team (VDT) research group at Stanford University (USA), the Systems Engineering Group (SEG) at De Montfort University (UK) and Elipsis Ltd. We describe a new docking methodology in which we combine the use of two radically different types of organizational simulation tool. The VDT simulation tool operates on...

Protein–ligand docking is the major workhorse in computeraided structure-based lead finding and optimization. Predicted protein–ligand complex configurations are used for studying protein–ligand interactions, estimating binding affinities, and as a final filter step in virtual screening. Early methods on protein–ligand docking treated either both proteins and ligands as rigid molecules or allow...

Plants are simultaneously subjected to a variety of stress conditions in the field and are known to combat the hostile conditions by up/down-regulating number of genes. There exists a significant level of cross-talk between different stress responses in plants. In this study, we predict the interacting pairs of transcription factors that regulate the multiple abiotic stress-responsive genes in ...

We herewith present a novel approach to predict protein-ligand binding modes from the single two-dimensional structure of the ligand. Known protein-ligand X-ray structures were converted into binary bit strings encoding protein-ligand interactions. An artificial neural network was then set up to first learn and then predict protein-ligand interaction fingerprints from simple ligand descriptors....

In this paper, using the technique of docking, we perform verification & validation (V&V) of agent-based simulation models that simulate the life cycle of Anopheles gambiae, the primary vector for malaria transmission. Working with one (out of several) particular version of the core conceptual simulation model, we perform: (1) verification between two separate implementations (Java & C++) built...

In neurosecretory cells, secretory vesicles (SVs) undergo Ca(2+)-dependent fusion with the plasma membrane to release neurotransmitters. How SVs cross the dense mesh of the cortical actin network to reach the plasma membrane remains unclear. Here we reveal that, in bovine chromaffin cells, SVs embedded in the cortical actin network undergo a highly synchronized transition towards the plasma mem...

We have previously validated a probabilistic framework that combined computational approaches for predicting the biological activities of small molecule drugs. Molecule comparison methods included molecular structural similarity metrics and similarity computed from lexical analysis of text in drug package inserts. Here we present an analysis of novel drug/target predictions, focusing on those t...

monoamine oxidase (ec, 1.4.3.4) or amine oxidoreductase catalyzes the oxidative deamination of biogenic amines. abnormal action of the monoamine oxidase b has been associated with neurological dysfunctions including parkinson´s disorder. monoamine oxidase b inhibitors divulged that these agents were effective in the therapeutic management of parkinson's disease. understanding the interaction of...