GraphBNC source code
GraphBNC lähdekoodi
Pihlajamäki, Antti; Malola, Sami; Matus Cortés, Maria; Häkkinen, Hannu. GraphBNC source code. V. 19.6.2024. University of Jyväskylä. 10.17011/jyx/dataset/96312
Päivämäärä
2024Tekijänoikeudet
Pihlajamäki, Antti and University of Jyväskylä
GraphBNC is a framework that combines graph theory based methods, machine learning and other computational tools for placing protected gold nanoclusters on blood proteins. Machine learning part, artificial neural networks (ANNs) in this case, estimates interactions between the ligand molecules of the nanocluster and amino acid residues, which are used to find favorable site for the nanocluster on the protein. This dataset contains basic source codes needed to run the method. The first part contains methods to encode the nanoclusters and the proteins. The second part has the codes to train and to test ANNs, but pretrained weights are also provided. The rest focuses on the placement of the cluster utilizing Monte Carlo -based simulated annealing.
This is a snapshot of the code dataset that has been taken on 05.07.2024. A more detailed description of the data and the address to the GitLab repository for the latest version of the code can be found from the parent dataset of this data publication. The dataset is published under a GNU Affero General Public License 3.
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Julkaisija
University of JyväskyläKuuluu aineistoon
Pihlajamäki, Antti; Malola, Sami; Matus Cortés, Maria; Häkkinen, Hannu. GraphBNC source code (parent repository). V. 19.6.2024. University of Jyväskylä. https://gitlab.jyu.fi/graphbnc-project-group/graphbnc. https://doi.org/10.17011/jyx/dataset/96311Asiasanat
Aineisto tutkimustietojärjestelmässä
https://converis.jyu.fi/converis/portal/detail/ResearchDataset/220808845
Metadata
Näytä kaikki kuvailutiedotKokoelmat
- Tutkimusdata [274]
Rahoittaja(t)
Research Council of Finland; Suomen AkatemiaRahoitusohjelmat(t)
Others, AoF; Muut, SALisenssi
Ellei muuten mainita, aineiston lisenssi on GNU Affero General Public License 3
Samankaltainen aineisto
Näytetään aineistoja, joilla on samankaltainen nimeke tai asiasanat.
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GraphBNC source code (parent repository)
Pihlajamäki, Antti; Matus Cortés, Maria; Malola, Sami; Häkkinen, Hannu (University of Jyväskylä, 2024)GraphBNC is a framework that combines graph theory based methods, machine learning and other computational tools for placing protected gold nanoclusters on blood proteins. Machine learning part, artificial neural networks ... -
Kernels and Graphs on M25 + H (parent repository)
Häkkinen, Hannu; Kärkkäinen, Tommi; Pihlajamäki, Antti; Malola, Sami (University of Jyväskylä, 2023)The repository contains codes related to article "Graphs and Kernelized Learning Applied to Interactions of Hydrogen with Doped Gold Nanoparticle Electrocatalysts". There are two main types of codes: codes to transform a ... -
Kernels and Graphs on M25 + H
Kärkkäinen, Tommi; Häkkinen, Hannu; Malola, Sami; Pihlajamäki, Antti (University of Jyväskylä, 2023)Codes related to article "Graphs and Kernelized Learning Applied to Interactions of Hydrogen with Doped Gold Nanoparticle Electrocatalysts". There are two main types of codes: codes to transform a catalytic system of ... -
2023 Roadmap on molecular modelling of electrochemical energy materials
Zhang, Chao; Cheng, Jun; Chen, Yiming; Chan, Maria K. Y.; Cai, Qiong; Carvalho, Rodrigo P.; Marchiori, Cleber F. N.; Brandell, Daniel; Araujo, C. Moyses; Chen, Ming; Ji, Xiangyu; Feng, Guang; Goloviznina, Kateryna; Serva, Alessandra; Salanne, Mathieu; Mandai, Toshihiko; Hosaka, Tomooki; Alhanash, Mirna; Johansson, Patrik; Qiu, Yun-Ze; Xiao, Hai; Eikerling, Michael; Jinnouchi, Ryosuke; Melander, Marko M.; Kastlunger, Georg; Bouzid, Assil; Pasquarello, Alfredo; Shin, Seung-Jae; Kim, Minho M.; Kim, Hyungjun; Schwarz, Kathleen; Sundararaman, Ravishankar (IOP Publishing, 2023)New materials for electrochemical energy storage and conversion are the key to the electrification and sustainable development of our modern societies. Molecular modelling based on the principles of quantum mechanics and ... -
Nanodevices by DNA based gold nanostructures
Tapio, Kosti (University of Jyväskylä, 2017)In this thesis DNA based structures were utilized to create gold nanostructures for nanosensing and nanoelectronic applications. In the past, both of these fields have been dominated by the conventional lithography methods, ...
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