AIMC Topic: Biological Transport

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OMPcontact: An Outer Membrane Protein Inter-Barrel Residue Contact Prediction Method.

Journal of computational biology : a journal of computational molecular cell biology
In the two transmembrane protein types, outer membrane proteins (OMPs) perform diverse important biochemical functions, including substrate transport and passive nutrient uptake and intake. Hence their 3D structures are expected to reveal these funct...

Development of a Support Vector Machine-Based System to Predict Whether a Compound Is a Substrate of a Given Drug Transporter Using Its Chemical Structure.

Journal of pharmaceutical sciences
The aim of this study was to develop an in silico prediction system to assess which of 7 categories of drug transporters (organic anion transporting polypeptide [OATP] 1B1/1B3, multidrug resistance-associated protein [MRP] 2/3/4, organic anion transp...

Predicting lymphatic transport potential using graph transformer based on limited historical data from in vivo studies.

Journal of controlled release : official journal of the Controlled Release Society
The lymphatic system hosts a large number of therapeutic targets that can be used to modulate a wide range of diseases including cancers, autoimmune and inflammatory disorders, infectious diseases and metabolic syndrome; however, drug access to the l...

A merged molecular representation deep learning method for blood-brain barrier permeability prediction.

Briefings in bioinformatics
The ability of a compound to permeate across the blood-brain barrier (BBB) is a significant factor for central nervous system drug development. Thus, for speeding up the drug discovery process, it is crucial to perform high-throughput screenings to p...

Relational graph convolutional networks for predicting blood-brain barrier penetration of drug molecules.

Bioinformatics (Oxford, England)
MOTIVATION: Evaluating the blood-brain barrier (BBB) permeability of drug molecules is a critical step in brain drug development. Traditional methods for the evaluation require complicated in vitro or in vivo testing. Alternatively, in silico predict...

LightBBB: computational prediction model of blood-brain-barrier penetration based on LightGBM.

Bioinformatics (Oxford, England)
MOTIVATION: Identification of blood-brain barrier (BBB) permeability of a compound is a major challenge in neurotherapeutic drug discovery. Conventional approaches for BBB permeability measurement are expensive, time-consuming and labor-intensive. BB...

Classification of particle trajectories in living cells: Machine learning versus statistical testing hypothesis for fractional anomalous diffusion.

Physical review. E
Single-particle tracking (SPT) has become a popular tool to study the intracellular transport of molecules in living cells. Inferring the character of their dynamics is important, because it determines the organization and functions of the cells. For...

Planning Framework for Robot-assisted Blood-Brain Barrier Opening with Focused Ultrasound.

Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference
This article presents a method to plan BloodBrain Barrier (BBB) disruption with Focused Ultrasound, under neuronavigated robotic assistance. Robotic and acoustic constraints are defined to estimate brain target accessibility. The relevance of the pro...

Schwann Cell and Axon: An Interlaced Unit-From Action Potential to Phenotype Expression.

Advances in experimental medicine and biology
Here we propose a model of a peripheral axon with a great deal of autonomy from its cell body-the autonomous axon-but with a substantial dependence on its ensheathing Schwann cell (SC), the axon-SC unit. We review evidence in several fields and show ...