Related papers: MolWorld: Molecule World Models for Actionable Mol…

Recent advances in machine learning for molecules exhibit great potential for facilitating drug discovery from in silico predictions. Most models for molecule generation rely on the decomposition of molecules into frequently occurring…

Molecular dynamics simulations are a cornerstone in science, allowing to investigate from the system's thermodynamics to analyse intricate molecular interactions. In general, to create extended molecular trajectories can be a…

Efficient structure search is a major challenge in computational materials science. We present a modification of the basin hopping global geometry optimization approach that uses a curvilinear coordinate system to describe global trial…

Optimal curve methods provide a fundamental framework for tubular centerline tracking. Point-wise approaches, such as minimal paths, are theoretically elegant but often suffer from shortcut and short-branch combination problems in complex…

Designing a single neural network architecture that performs competitively across a range of molecule property prediction tasks remains largely an open challenge, and its solution may unlock a widespread use of deep learning in the drug…

Molecular machine learning has been maturing rapidly over the last few years. Improved methods and the presence of larger datasets have enabled machine learning algorithms to make increasingly accurate predictions about molecular…

We investigate improving Monte Carlo Tree Search based solvers for Partially Observable Markov Decision Processes (POMDPs), when applied to adaptive sampling problems. We propose improvements in rollout allocation, the action exploration…

Machine learning (ML) is a promising approach for predicting small molecule properties in drug discovery. Here, we provide a comprehensive overview of various ML methods introduced for this purpose in recent years. We review a wide range of…

Molecular optimization is a crucial aspect of drug discovery, aimed at refining molecular structures to enhance drug efficacy and minimize side effects, ultimately accelerating the overall drug development process. Many molecular…

Molecular Dynamics (MD) simulations are ubiquitous in cutting-edge physio-chemical research. They provide critical insights into how a physical system evolves over time given a model of interatomic interactions. Understanding a system's…

We revisit the effectiveness of topological descriptors for molecular graph classification and design a simple, yet strong baseline. We demonstrate that a simple approach to feature engineering - employing histogram aggregation of edge…

Computational molecular design -- the endeavor to design molecules, with various missions, aided by machine learning and molecular dynamics approaches, has been widely applied to create valuable new molecular entities, from small molecule…

Neural methods of molecule property prediction require efficient encoding of structure and property relationship to be accurate. Recent work using graph algorithms shows limited generalization in the latent molecule encoding space. We build…

Molecules have a number of distinct properties whose importance and application vary. Often, in reality, labels for some properties are hard to achieve despite their practical importance. A common solution to such data scarcity is to use…

The efficacy of a drug depends on its binding affinity to the therapeutic target and pharmacokinetics. Deep learning (DL) has demonstrated remarkable progress in predicting drug efficacy. We develop MolDesigner, a human-in-the-loop web…

Molecular representation learning is crucial for the problem of molecular property prediction, where graph neural networks (GNNs) serve as an effective solution due to their structure modeling capabilities. Since labeled data is often…

With the prospect of automating a number of chemical tasks with high fidelity, chemical language processing models are emerging at a rapid speed. Here, we present a cloud-based real-time platform that allows users to virtually screen…

The ability to design molecules while preserving similarity to a target molecule and/or property is crucial for various applications in drug discovery, chemical design, and biology. We introduce in this paper an efficient training-free…

Theoretical concepts in condensed matter physics are typically verified and also developed by exploiting computer simulations mostly in simple models. Predictions based on these usually isotropic models are often at odds with measurement…

Molecule design is a multifaceted approach that leverages computational methods and experiments to optimize molecular properties, fast-tracking new drug discoveries, innovative material development, and more efficient chemical processes.…