Radheesh Sharma Meda

Achuth Chandrasekhar, Omid Barati Farimani, Radheesh Sharma Meda et al.

Materials science workflows rely on structured and unstructured data from the vast body of available scientific literature. However, most of the experimental details remain buried in text, tables, graphs and figures. Thus, constructing databases that incorporate this data is a manual, time-consuming, and hard-to-scale process. Multimodal large language models have made it feasible to extract information from text and scientific figures with high speed and accuracy. This opens the possibility of an AI system that can create production-scale material databases. Material Database Agent (MDA) is a modular, multi-agent system architecture for converting research literature into structured databases. MDA accepts article PDFs as input, which are subsequently processed in parallel into markdown files and figures. Multiple sub-agents read these markdown files and figures in parallel to assemble sub-databases for each paper. These sub-databases are then compiled into a single tabular database by an agent. As opposed to using either a rule-based approach or a single-pass pipeline for extracting information, MDA is a specialized architecture for transforming the literature into a database in the field of materials science. More generally, this study provides a basis for positioning multimodal agentic information extraction as a viable means for constructing next-generation scientific databases from the primary literature.

Srivathsan Badrinarayanan, Rishikesh Magar, Akshay Antony et al.

The discovery of Metal-Organic Frameworks (MOFs) with application-specific properties remains a central challenge in materials chemistry, owing to the immense size and complexity of their structural design space. Conventional computational screening techniques such as molecular simulations and density functional theory (DFT), while accurate, are computationally prohibitive at scale. Machine learning offers an exciting alternative by leveraging data-driven approaches to accelerate materials discovery. The complexity of MOFs, with their extended periodic structures and diverse topologies, creates both opportunities and challenges for generative modeling approaches. To address these challenges, we present a reinforcement learning-enhanced, transformer-based framework for the de novo design of MOFs. Central to our approach is MOFid, a chemically-informed string representation encoding both connectivity and topology, enabling scalable generative modeling. Our pipeline comprises three components: (1) a generative GPT model trained on MOFid sequences, (2) MOFormer, a transformer-based property predictor, and (3) a reinforcement learning (RL) module that optimizes generated candidates via property-guided reward functions. By integrating property feedback into sequence generation, our method drives the model toward synthesizable, topologically valid MOFs with desired functional attributes. This work demonstrates the potential of large language models, when coupled with reinforcement learning, to accelerate inverse design in reticular chemistry and unlock new frontiers in computational MOF discovery.

Janghoon Ock, Radheesh Sharma Meda, Tirtha Vinchurkar et al.

Adsorption energy is a key reactivity descriptor in catalysis. Determining adsorption energy requires evaluating numerous adsorbate-catalyst configurations, making it computationally intensive. Current methods rely on exhaustive sampling, which does not guarantee the identification of the global minimum energy. To address this, we introduce Adsorb-Agent, a Large Language Model (LLM) agent designed to efficiently identify stable adsorption configurations corresponding to the global minimum energy. Adsorb-Agent leverages its built-in knowledge and reasoning to strategically explore configurations, significantly reducing the number of initial setups required while improving energy prediction accuracy. In this study, we also evaluated the performance of different LLMs, including GPT-4o, GPT-4o-mini, Claude-3.7-Sonnet, and DeepSeek-Chat, as the reasoning engine for Adsorb-Agent, with GPT-4o showing the strongest overall performance. Tested on twenty diverse systems, Adsorb-Agent identifies comparable adsorption energies for 84% of cases and achieves lower energies for 35%, particularly excelling in complex systems. It identifies lower energies in 47% of intermetallic systems and 67% of systems with large adsorbates. These findings demonstrate Adsorb-Agent's potential to accelerate catalyst discovery by reducing computational costs and enhancing prediction reliability compared to exhaustive search methods.

Janghoon Ock, Radheesh Sharma Meda, Srivathsan Badrinarayanan et al.

We present a modular framework powered by large language models (LLMs) that automates and streamlines key tasks across the early-stage computational drug discovery pipeline. By combining LLM reasoning with domain-specific tools, the framework performs biomedical data retrieval, domain-specific question answering, molecular generation, property prediction, property-aware molecular refinement, and 3D protein-ligand structure generation. In a case study targeting BCL-2 in lymphocytic leukemia, the agent autonomously retrieved relevant biomolecular information, including FASTA sequences, SMILES representations, and literature, and answered mechanistic questions with improved contextual accuracy compared to standard LLMs. It then generated chemically diverse seed molecules and predicted 67 ADMET-related properties, which guided iterative molecular refinement. Across two refinement rounds, the number of molecules with QED > 0.6 increased from 34 to 55. The number of molecules satisfying empirical drug-likeness filters also rose; for example, compliance with the Ghose filter increased from 32 to 55 within a pool of 100 molecules. The framework also employed Boltz-2 to generate 3D protein-ligand complexes and provide rapid binding affinity estimates for candidate compounds. These results demonstrate that the approach effectively supports molecular screening, prioritization, and structure evaluation. Its modular design enables flexible integration of evolving tools and models, providing a scalable foundation for AI-assisted therapeutic discovery.

Radheesh Sharma Meda, Amir Barati Farimani

Identifying drug-target interactions is essential for developing effective therapeutics. Binding affinity quantifies these interactions, and traditional approaches rely on computationally intensive 3D structural data. In contrast, language models can efficiently process sequential data, offering an alternative approach to molecular representation. In the current study, we introduce BAPULM, an innovative sequence-based framework that leverages the chemical latent representations of proteins via ProtT5-XL-U50 and ligands through MolFormer, eliminating reliance on complex 3D configurations. Our approach was validated extensively on benchmark datasets, achieving scoring power (R) values of 0.925 $\pm$ 0.043, 0.914 $\pm$ 0.004, and 0.8132 $\pm$ 0.001 on benchmark1k2101, Test2016_290, and CSAR-HiQ_36, respectively. These findings indicate the robustness and accuracy of BAPULM across diverse datasets and underscore the potential of sequence-based models in-silico drug discovery, offering a scalable alternative to 3D-centric methods for screening potential ligands.