Scientific workflows: moving across paradigms

CS Liew, MP Atkinson, M Galea, TF Ang… - ACM Computing …, 2016 - dl.acm.org
Modern scientific collaborations have opened up the opportunity to solve complex problems
that require both multidisciplinary expertise and large-scale computational experiments …

Apache airavata: a framework for distributed applications and computational workflows

S Marru, L Gunathilake, C Herath… - Proceedings of the …, 2011 - dl.acm.org
In this paper, we introduce Apache Airavata, a software framework to compose, manage,
execute, and monitor distributed applications and workflows on computational resources …

Paramfit: Automated optimization of force field parameters for molecular dynamics simulations

RM Betz, RC Walker - Journal of computational chemistry, 2015 - Wiley Online Library
The generation of bond, angle, and torsion parameters for classical molecular dynamics
force fields typically requires fitting parameters such that classical properties such as …

Apache Airavata: design and directions of a science gateway framework

M Pierce, S Marru, L Gunathilake… - … workshop on science …, 2014 - ieeexplore.ieee.org
This paper provides an overview of the Apache Airavata software system for science
gateways. Gateways use Airavata to manage application and workflow executions on a …

Submolecular probing of the complement C5a receptor–ligand binding reveals a cooperative two-site binding mechanism

AC Dumitru, RNVK Deepak, H Liu, M Koehler… - Communications …, 2020 - nature.com
A current challenge to produce effective therapeutics is to accurately determine the location
of the ligand-biding site and to characterize its properties. So far, the mechanisms …

From Static to Dynamic Structures: Improving Binding Affinity Prediction with Graph‐Based Deep Learning

Y Min, Y Wei, P Wang, X Wang, H Li, N Wu… - Advanced …, 2024 - Wiley Online Library
Accurate prediction of protein‐ligand binding affinities is an essential challenge in structure‐
based drug design. Despite recent advances in data‐driven methods for affinity prediction …

Laparoscopic virtual mirror new interaction paradigm for monitor based augmented reality

N Navab, M Feuerstein… - 2007 IEEE Virtual Reality …, 2007 - ieeexplore.ieee.org
A major roadblock for using augmented reality in many medical and industrial applications is
the fact that the user cannot take full advantage of the 3D virtual data. This usually requires …

A least-squares-fitting procedure for an efficient preclinical ranking of passive transport across the blood–brain barrier endothelium

C Jorgensen, EP Troendle, JP Ulmschneider… - Journal of Computer …, 2023 - Springer
The treatment of various disorders of the central nervous system (CNS) is often impeded by
the limited brain exposure of drugs, which is regulated by the human blood–brain barrier …

Atomistic model of solute transport across the blood–brain barrier

C Jorgensen, MB Ulmschneider, PC Searson - ACS omega, 2021 - ACS Publications
The blood–brain barrier remains a major roadblock to the delivery of drugs to the brain.
While in vitro and in vivo measurements of permeability are widely used to predict brain …

A credential store for multi-tenant science gateways

TA Kanewala, S Marru, J Basney… - 2014 14th IEEE/ACM …, 2014 - ieeexplore.ieee.org
Science Gateways bridge multiple computational grids and clouds, acting as overlay cyber
infrastructure. Gateways have three logical tiers: a user interfacing tier, a resource tier and a …