A5067172880- Scientific Computing and Data Management
- Protein Structure and Dynamics
- Machine Learning in Materials Science
- Block Copolymer Self-Assembly
- Material Dynamics and Properties
- Theoretical and Computational Physics
- Radiomics and Machine Learning in Medical Imaging
- Enhanced Oil Recovery Techniques
- Distributed and Parallel Computing Systems
- Parallel Computing and Optimization Techniques
- Advanced Data Storage Technologies
- Digital Imaging for Blood Diseases
- Mass Spectrometry Techniques and Applications
- Computational Drug Discovery Methods
- Polymer crystallization and properties
- Gene expression and cancer classification
- Conservation, Biodiversity, and Resource Management
- Advanced Mathematical Modeling in Engineering
- Zeolite Catalysis and Synthesis
- Carbon Dioxide Capture Technologies
- Bioinformatics and Genomic Networks
- Research Data Management Practices
- Medical Imaging Techniques and Applications
- Image Retrieval and Classification Techniques
- Analytical Chemistry and Sensors
Open Molecular Software Foundation
2022-2024
Open Geospatial Consortium
2024
University of New Hampshire
2019-2020
University of New Hampshire at Manchester
2019
Rutgers, The State University of New Jersey
2019
University of Edinburgh
2016-2017
Arizona State University
2016
Université de Picardie Jules Verne
2016
University of Manchester
2014-2016
UNSW Sydney
2003
MDAnalysis (http://mdanalysis.org) is a library for structural and temporal analysis of molecular dynamics (MD) simulation trajectories individual protein structures. MD simulations biological molecules have become an important tool to elucidate the relationship between structure physiological function. Simulations are performed with highly optimized software packages on HPC resources but most codes generate output in their own formats so that development new trajectory algorithms confined...
We present a simple multiscale model for polymer chains in which it is possible to selectively remove degrees of freedom. The integrates all-atom and coarse-grained potentials systematic way allows fast sampling the complex conformational energy surface typical polymers whilst maintaining realistic description selected atomistic interactions. In particular, we show that simultaneously reproduce structure highly directional non-bonded interactions such as hydrogen bonds efficiently explore...
In this work we set out to evaluate the computational performance of several popular Monte Carlo simulation programs, namely Cassandra, DL Monte, Music, Raspa and Towhee, in modelling gas adsorption crystalline materials. We focus on reference case IRMOF-1 at 208 K. To critically assess their performance, first establish some criteria which allow us make assessment a consistent basis. Specifically, total time required for program complete an point, consists equilibration plus generate...
Small-molecule lead optimisation in early-stage drug discovery is broadly supported by computational chemistry approaches throughout industry. Over the last decade, Free Energy Perturbation (FEP) has grown into a mature physics-based tool that prospectively guides medicinal decision-making accurately predicting ligand potencies at level of precision required for granular nature stage. Machine-learned ligand-protein co-folding models are forefront accurate protein structure prediction and...
Small-molecule lead optimisation in early-stage drug discovery is broadly supported by computational chemistry approaches throughout industry. Over the last decade, Free Energy Perturbation (FEP) has grown into a mature physics-based tool that prospectively guides medicinal decision-making accurately predicting ligand potencies at level of precision required for granular nature stage. Machine-learned ligand-protein co-folding models are forefront accurate protein structure prediction and...
Relative binding free energy (RBFE) calculations have emerged as a powerful tool that supports ligand optimization in drug discovery. Despite many successes, the use of RBFEs can often be limited by automation problems, particular, setup such calculations. Atom mapping algorithms are an essential component setting up automatic large-scale hybrid-topology RBFE calculation campaigns. Traditional typically employ 2D subgraph isomorphism solver (SIS) order to estimate maximum common...
The development of rational crystallisation strategies in polymorphic systems requires the experimental manipulation both kinetics and thermodynamics.
In science the filesystem often serves as a de facto database, with directory trees being zeroth-order scientific data structure. But it can be tedious and error prone to work directly retrieve store heterogeneous datasets. datreant makes working structures files Pythonic Treants: specially marked directories distinguishing characteristics that discovered, queried, filtered. Treants manipulated individually in aggregate, mechanisms for granular access their trees. Disparate datasets stored...
In hybrid particle models where coarse‐grained beads and atoms are used simultaneously, two clearly separate time scales mixed. If such in molecular dynamics simulations, a multiple step (MTS) scheme can therefore be used. this manuscript, we propose simple MTS algorithm which approximates for specific number of integration steps the slow bead–bead interactions with Taylor series approximation while atom–atom ones integrated every step. The procedure is applied to previously developed model...
MDAnalysis is an object-oriented Python library to analyze trajectories from molecular dynamics (MD) simulations in many popular formats. With the development of highly optimized MD software packages on high performance computing (HPC) resources, size simulation growing up terabytes size. However efficient usage multicore architecture a challenge for MDAnalysis, which does not yet provide standard interface parallel analysis. To address challenge, we developed PMDA, that builds upon analysis...
This release fixes a subtle but important issue caused by missing file when PyPi Tarball was compiled from Python 3, then downloaded in 2 Because this changes the setup.py file, formal cut.
Alchemical free energy campaigns can be planned using graph theory by building up networks that contain nodes representing molecules are connected possible transformations as edges. We introduce Konnektor, an open-source Python package, for systematically planning, modifying, and analyzing calculation networks. Konnektor is designed to aid in the drug discovery process enabling users easily setup complex manipulation methods. The package contains functions network operations including...
Alchemical free energy campaigns can be planned using graph theory by building networks that contain nodes representing molecules are connected possible transformations as edges. We introduce Konnektor, an open-source Python package, for systematically planning, modifying, and analyzing calculation networks. Konnektor is designed to aid in the drug discovery process enabling users easily setup complex manipulation methods. The package contains functions network operations including...
The reproducibility and transparency of scientific findings are widely recognized as crucial for promoting progress. However, when it comes to software, researchers face many barriers few incentives ensure that their software is open the community, thoroughly tested, easily accessible. To address this issue, MDAKits framework has been developed, which simplifies process creating toolkits MDAnalysis simulation analysis package (https://www.mdanalysis.org/) follow basic principles FAIR...
Relative binding free energy (RBFE) calculations have emerged as a powerful tool supporting ligand optimization in drug discovery. Despite many successes, the use of RBFEs can often be limited by automation problems, particular setup such calculations. Atom mapping algorithms are an essential component setting up automatic large-scale hybrid topology RBFE calculation campaigns. Traditional typically employ 2D subgraph isomorphism solver (SIS) order to estimate maximum common substructure...
Abstract Between 1915 and 1961 a state-run trawling industry operated on the South-east Australian shelf targeting tiger flathead (Neoplatycephalus richardsoni) as its principal species. When last steam-trawlers left in 1961, stocks had effectively collapsed. The familiar experience of overfishing, however, was due much to social cultural pressures it increasing numbers fishers delicate species with ever improving technologies. Flathead declined direct result government initiative, designed...