PepBAN is introduced, a deep learning framework for modeling PepPI predictions that effectively learns the pattern of pairwise local interactions, enables the identification of key residues participating in the peptide-protein interactions, and offers an intuitive approach to interpret the underlying mechanisms of PepP...
Shuaiyan Li, Xiaorui Wang, Yuchen Zhu et al.· Journal of Chemical Informat...· 4 citations
This study proposes SynGFN, which models molecular design as a cascade of simulated chemical reactions, enabling the assembly of molecules from synthesizable building blocks, as a bridge linking molecular design and synthesis, accelerating exploration and producing diverse, synthesizable, high-performance molecules.
Results indicate that BF3 antagonists can synergize with the LBP antagonist to amplify conformational flexibility in H12 and induce anticorrelated dynamics of H12 with H3 and H4, suggesting a promising avenue for enhancing the efficacy and overcoming the resistance in castration-resistant prostate cancer treatment.
Xiaotian Kong, Yushan Zou, Peng Cao et al.· Journal of Chemical Informat...· 1 citation
This work introduces an advanced equivariant graph attention neural network specifically engineered to model long-range atomic electrostatic interactions with high precision, and improves the model's accuracy, generalization, and robustness in complex scenarios.
Qiaolin Gou, Qun Su, Ji-Ke Wang et al.· Journal of Chemical Informat...· 1 citation
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PepPCBench enables a robust evaluation of PFNN-based methods and supports their continued development for peptide-protein structure prediction, and highlights the influence of peptide length, conformational flexibility, and training set similarity on prediction accuracy.
Si-Long Zhai, Huifeng Zhao, Ji-Ke Wang et al.· Journal of Chemical Informat...· 13 citations· ⚡1
The Q‐GEM comprises a GNN embedded with the molecular electronic and complete 3D geometrical structural information as well as several well‐designed multiscale SSL tasks, achieving superior absolute molecular conformation prediction and conformational discrimination.
Zhijiang Yang, Liangliang Wang, Tengxin Huang et al.· Advancement of science· 6 citations
This study established a unified model (NRIGN) based on the deep graphic architecture to discriminate agonists and antagonists targeting 26 successful or in-clinical-trial NR targets and achieves an excellent prediction accuracy and is robust enough to be applied in various real-world scenarios.
Kaimo Yang, Dejun Jiang, Qirui Deng et al.· Journal of Chemical Informat...· 2 citations
This study presents ECloudGen, which uses latent diffusion to generate electron clouds from protein pockets and decodes them into molecules, and adopts two-stage training, which expands the chemical space accessible to generative drug design.
Abstract Cyclic peptides represent a highly promising class of biopharmaceutical scaffolds. The screening of cyclic peptides against protein targets can be greatly facilitated using computational approaches, especially molecular docking. However, it remains a crucial challenge to accurately predict protein–cyclic pepti...
A unified benchmarking framework is established that enables systematic evaluation of docking methods across diverse tasks and provides critical insights into the strengths and limitations of current docking strategies, thereby informing future developments in protein-protein docking research.
Linlong Jiang, Ke Zhang, Kai Zhu et al.· Journal of Chemical Informat...· 3 citations
Macrocycle-DB is presented, the most extensive online database dedicated to macrocycles, featuring 45 525 compounds, including 76 approved drugs and 105 clinical candidates that target 2533 proteins.
NavDB is a specialized and open-access database focusing on VGSC modulators and targets that integrates 8023 curated data records covering 5168 compounds, including small molecules, toxins, drugs, and peptides, along with comprehensive annotations on biological activity, druggability, and structural feature.
Gaoang Wang, Jiahui Yu, Haiyi Chen et al.· Journal of Chemical Informat...· 0 citations
AI agents can generate code at a scale that’s hard for humans to review line-by-line. PDD Kit helps ensure the code is doing what the developer intended by creating formal specifications and testing against them. It converts developer intent into a Verus specification, proves AI-generated code meets it for every input, and uses tests where proofs aren't practical. Developers review intent, not every line. The post Formally verifying agent-written full-stack web apps with PDD Kit appeared first o…
Professor Paris Smaragdis develops computers with superhuman hearing for applications like speech recognition, music understanding, and environmental monitoring.
MIT News · Artificial Intelligence· news.mit.eduOct 23, 2026
During the School of Humanities, Arts, and Social Sciences’ 75th Anniversary Symposium, President Sally Kornbluth said “MIT has never needed your particular insight and guidance more than we do now.”
MIT News · Artificial Intelligence· news.mit.eduOct 23, 2026
Assistant Professor Benjamin Lindquist studies how engineers deliberately injected randomness into early AI, giving rise to deep-learning models that sometimes hallucinate.
MIT News · Artificial Intelligence· news.mit.eduOct 22, 2026
“X-Hinges” helps design and 3D print items like lamps and gloves with an interactive twist: automatically embedded sensors that perceive and adaptively respond to human contact.
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