A key challenge in protein engineering is understanding how mutations affect protein fitness and stability. Most of current state-of-the-art models fine-tune protein structure prediction or protein language models or even pretrain their own. Despite its widespread use within computational workflows, AlphaFold2 exhibits limited sensitivity in assessing the effects of amino acid point mutations on protein structure, thereby constraining its utility in sequence design and protein engineering. In this work, we propose a simple modification of AlphaFold2 inference that improves the model's capacity to capture the structural impacts of amino acid mutations. We achieve this by discarding the multiple sequence alignment and masking the template in recycling stages. Moreover, we introduce AFToolkit, a framework that leverages the embeddings of the modified AlphaFold2 model and simple adapter models to solve multiple protein engineering tasks. In contrast to other methods, our approach does not require fine-tuning the AlphaFold2 model or pretraining a new model from scratch on large datasets. It also supports handling multiple mutations, insertions, and deletions by directly modifying the input protein sequence. The proposed approach achieves strong performance across established benchmarks in terms of Spearman correlation: $0.68$ on PTMul, $0.60$ on cDNA-indel, and $0.57$ on C380.

Molecular conformation optimization is crucial to computer-aided drug discovery and materials design. Traditional energy minimization techniques rely on iterative optimization methods that use molecular forces calculated by a physical simulator (oracle) as anti-gradients. However, this is a computationally expensive approach that requires many interactions with a physical simulator. One way to accelerate this procedure is to replace the physical simulator with a neural network. Despite recent progress in neural networks for molecular conformation energy prediction, such models are prone to errors due to distribution shift, leading to inaccurate energy minimization. We find that the quality of energy minimization with neural networks can be improved by providing optimization trajectories as additional training data. Still, obtaining complete optimization trajectories demands a lot of additional computations. To reduce the required additional data, we present the Gradual Optimization Learning Framework (GOLF) for energy minimization with neural networks. The framework consists of an efficient data-collecting scheme and an external optimizer. The external optimizer utilizes gradients from the energy prediction model to generate optimization trajectories, and the data-collecting scheme selects additional training data to be processed by the physical simulator. Our results demonstrate that the neural network trained with GOLF performs \textit{on par} with the oracle on a benchmark of diverse drug-like molecules using significantly less additional data.

Methods of computational quantum chemistry provide accurate approximations of molecular properties crucial for computer-aided drug discovery and other areas of chemical science. However, high computational complexity limits the scalability of their applications.Neural network potentials (NNPs) are a promising alternative to quantum chemistry methods, but they require large and diverse datasets for training.This work presents a new dataset and benchmark called $\nabla^2$DFT that is based on the nablaDFT.It contains twice as much molecular structures, three times more conformations, new data types and tasks, and state-of-the-art models.The dataset includes energies, forces, 17 molecular properties, Hamiltonian and overlap matrices, and a wavefunction object.All calculations were performed at the DFT level ($\omega$B97X-D/def2-SVP) for each conformation. Moreover, $\nabla^2$DFT is the first dataset that contains relaxation trajectories for a substantial number of drug-like molecules. We also introduce a novel benchmark for evaluating NNPs in molecular property prediction, Hamiltonian prediction, and conformational optimization tasks. Finally, we propose an extendable framework for training NNPs and implement 10 models within it.

MOTIVATION: Clinical trials are the essential stage of every drug development program for the treatment to become available to patients. Despite the importance of well-structured clinical trial databases and their tremendous value for drug discovery and development such instances are very rare. Presently large-scale information on clinical trials is stored in clinical trial registers which are relatively structured, but the mappings to external databases of drugs and diseases are increasingly lacking. The precise production of such links would enable us to interrogate richer harmonized datasets for invaluable insights. RESULTS: We present a neural approach for medical concept normalization of diseases and drugs. Our two-stage approach is based on Bidirectional Encoder Representations from Transformers (BERT). In the training stage, we optimize the relative similarity of mentions and concept names from a terminology via triplet loss. In the inference stage, we obtain the closest concept name representation in a common embedding space to a given mention representation. We performed a set of experiments on a dataset of abstracts and a real-world dataset of trial records with interventions and conditions mapped to drug and disease terminologies. The latter includes mentions associated with one or more concepts (in-KB) or zero (out-of-KB, nil prediction). Experiments show that our approach significantly outperforms baseline and state-of-the-art architectures. Moreover, we demonstrate that our approach is effective in knowledge transfer from the scientific literature to clinical trial data. AVAILABILITY AND IMPLEMENTATION: We make code and data freely available at https://github.com/insilicomedicine/DILBERT.

Linking of biomedical entity mentions to various terminologies of chemicals, diseases, genes, adverse drug reactions is a challenging task, often requiring non-syntactic interpretation. A large number of biomedical corpora and state-of-the-art models have been introduced in the past five years. However, there are no general guidelines regarding the evaluation of models on these corpora in single- and cross-terminology settings. In this work, we perform a comparative evaluation of various benchmarks and study the efficiency of state-of-the-art neural architectures based on Bidirectional Encoder Representations from Transformers (BERT) for linking of three entity types across three domains: research abstracts, drug labels, and user-generated texts on drug therapy in English. We have made the source code and results available at https://github.com/insilicomedicine/Fair-Evaluation-BERT.