Search Results - "Bjerrum, Esben"

Improving Chemical Autoencoder Latent Space and Molecular De Novo Generation Diversity with Heteroencoders by Bjerrum, Esben Jannik, Sattarov, Boris

“…Chemical autoencoders are attractive models as they combine chemical space navigation with possibilities for de novo molecule generation in areas of interest…”
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Exploring Graph Traversal Algorithms in Graph-Based Molecular Generation by Mercado, Rocío, Bjerrum, Esben J., Engkvist, Ola

“…Here, we explore the impact of different graph traversal algorithms on molecular graph generation. We do this by training a graph-based deep molecular…”
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AiZynthFinder: a fast, robust and flexible open-source software for retrosynthetic planning by Genheden, Samuel, Thakkar, Amol, Chadimová, Veronika, Reymond, Jean-Louis, Engkvist, Ola, Bjerrum, Esben

“…We present the open-source AiZynthFinder software that can be readily used in retrosynthetic planning. The algorithm is based on a Monte Carlo tree search that…”
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Graph networks for molecular design by Mercado, Rocío, Rastemo, Tobias, Lindelöf, Edvard, Klambauer, Günter, Engkvist, Ola, Chen, Hongming, Jannik Bjerrum, Esben

“…Deep learning methods applied to chemistry can be used to accelerate the discovery of new molecules. This work introduces GraphINVENT, a platform developed for…”
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Machine learning optimization of cross docking accuracy by Bjerrum, Esben J.

“…[Display omitted] •Machine learning method for optimizing docking functions.•Alternative score weights for cross-docking with Autodock Vina and…”
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AI-assisted synthesis prediction by Johansson, Simon, Thakkar, Amol, Kogej, Thierry, Bjerrum, Esben, Genheden, Samuel, Bastys, Tomas, Kannas, Christos, Schliep, Alexander, Chen, Hongming, Engkvist, Ola

“…[Display omitted] Application of AI technologies in synthesis prediction has developed very rapidly in recent years. We attempt here to give a comprehensive…”
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LibINVENT: Reaction-based Generative Scaffold Decoration for in Silico Library Design by Fialková, Vendy, Zhao, Jiaxi, Papadopoulos, Kostas, Engkvist, Ola, Bjerrum, Esben Jannik, Kogej, Thierry, Patronov, Atanas

“…Because of the strong relationship between the desired molecular activity and its structural core, the screening of focused, core-sharing chemical libraries is…”
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Using Active Learning to Develop Machine Learning Models for Reaction Yield Prediction by Viet Johansson, Simon, Gummesson Svensson, Hampus, Bjerrum, Esben, Schliep, Alexander, Haghir Chehreghani, Morteza, Tyrchan, Christian, Engkvist, Ola

“…Computer aided synthesis planning, suggesting synthetic routes for molecules of interest, is a rapidly growing field. The machine learning methods used are…”
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Retrosynthetic accessibility score (RAscore) - rapid machine learned synthesizability classification from AI driven retrosynthetic planning by Thakkar, Amol, Chadimová, Veronika, Bjerrum, Esben Jannik, Engkvist, Ola, Reymond, Jean-Louis

“…Computer aided synthesis planning (CASP) is part of a suite of artificial intelligence (AI) based tools that are able to propose synthesis routes to a wide…”
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pICalculax: Improved Prediction of Isoelectric Point for Modified Peptides by Bjerrum, Esben J, Jensen, Jan H, Tolborg, Jakob L

“…The isoelectric point of a peptide is a physicochemical property that can be accurately predicted from the sequence of the peptide when the peptide is built…”
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A de novo molecular generation method using latent vector based generative adversarial network by Prykhodko, Oleksii, Johansson, Simon Viet, Kotsias, Panagiotis-Christos, Arús-Pous, Josep, Bjerrum, Esben Jannik, Engkvist, Ola, Chen, Hongming

“…Deep learning methods applied to drug discovery have been used to generate novel structures. In this study, we propose a new deep learning architecture,…”
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Randomized SMILES strings improve the quality of molecular generative models by Arús-Pous, Josep, Johansson, Simon Viet, Prykhodko, Oleksii, Bjerrum, Esben Jannik, Tyrchan, Christian, Reymond, Jean-Louis, Chen, Hongming, Engkvist, Ola

“…Recurrent Neural Networks (RNNs) trained with a set of molecules represented as unique (canonical) SMILES strings, have shown the capacity to create large…”
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SMILES-based deep generative scaffold decorator for de-novo drug design by Arús-Pous, Josep, Patronov, Atanas, Bjerrum, Esben Jannik, Tyrchan, Christian, Reymond, Jean-Louis, Chen, Hongming, Engkvist, Ola

“…Molecular generative models trained with small sets of molecules represented as SMILES strings can generate large regions of the chemical space. Unfortunately,…”
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Molecular optimization by capturing chemist’s intuition using deep neural networks by He, Jiazhen, You, Huifang, Sandström, Emil, Nittinger, Eva, Bjerrum, Esben Jannik, Tyrchan, Christian, Czechtizky, Werngard, Engkvist, Ola

“…A main challenge in drug discovery is finding molecules with a desirable balance of multiple properties. Here, we focus on the task of molecular optimization,…”
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Transformer-based molecular optimization beyond matched molecular pairs by He, Jiazhen, Nittinger, Eva, Tyrchan, Christian, Czechtizky, Werngard, Patronov, Atanas, Bjerrum, Esben Jannik, Engkvist, Ola

“…Molecular optimization aims to improve the drug profile of a starting molecule. It is a fundamental problem in drug discovery but challenging due to (i) the…”
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Metis: a python-based user interface to collect expert feedback for generative chemistry models by Menke, Janosch, Nahal, Yasmine, Bjerrum, Esben Jannik, Kabeshov, Mikhail, Kaski, Samuel, Engkvist, Ola

“…One challenge that current de novo drug design models face is a disparity between the user’s expectations and the actual output of the model in practical…”
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Human-in-the-loop assisted de novo molecular design by Sundin, Iiris, Voronov, Alexey, Xiao, Haoping, Papadopoulos, Kostas, Bjerrum, Esben Jannik, Heinonen, Markus, Patronov, Atanas, Kaski, Samuel, Engkvist, Ola

“…A de novo molecular design workflow can be used together with technologies such as reinforcement learning to navigate the chemical space. A bottleneck in the…”
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Medicines combinations options and regulatory hurdles by Bjerrum, Ole J., Gautam, Yvonne, Bjerrum, Esben J., Schmiegelow, Merete, Boonen, Harrie C.M.

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Applications of Deep-Learning in Exploiting Large-Scale and Heterogeneous Compound Data in Industrial Pharmaceutical Research by David, Laurianne, Arús-Pous, Josep, Karlsson, Johan, Engkvist, Ola, Bjerrum, Esben Jannik, Kogej, Thierry, Kriegl, Jan M, Beck, Bernd, Chen, Hongming

“…In recent years, the development of high-throughput screening (HTS) technologies and their establishment in an industrialized environment have given scientists…”
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Rigid body essential X-ray crystallography: Distinguishing the bend and twist of glutamate receptor ligand binding domains by Bjerrum, Esben J., Biggin, Philip C.

“…The ligand‐binding domain (LBD) from the ionotropic glutamate receptor subtype 2 (GluR2) has been shown to adopt a range of ligand‐dependent conformational…”
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