🧬 Weekly Recap

Jan 19 - Jan 23, 2026

Missed a day? Here are the top research signals and tools from Monday to Friday, summarized in one place.

🏆 Top Signals of the Week

🗓️ Friday, Jan 23

DynaBench: Dynamic data for the docking benchmark.

🧬 Abstract

Protein-protein interactions are central to numerous cellular processes, including transport, signaling, and immune response. Structural modeling of protein assemblies typically relies on AlphaFold or docking methods, which produce structural models evaluated against a single experimental reference. While AlphaFold2 and its extension, AlphaFold-Multimer, have advanced complex prediction, they, and conventional docking tools, offer only static representations. However, flexibility at protein-protein interfaces is increasingly recognized as critical for function. To address this limitation, DynaBench provides a benchmark of interface dynamics in biologically relevant protein assemblies. We performed MD simulations for over 200 protein-protein complexes listed in the Docking Benchmark 5.5 ( https://zlab.umassmed.edu/benchmark/), generating three 100 ns long replicas per complex. All trajectories are now publicly available online ( http://www-lbt.ibpc.fr/DynaBench) via the MDposit platform (INRIA node), which is part of the EU-funded Molecular Dynamics Data Bank (MDDB). These simulations offer a unique resource for exploring interfacial flexibility, training machine learning models, redefining accuracy metrics for model evaluation, and informing the design of protein interfaces.

Why it matters: Expands the searchable sequence space for novel folds and high-affinity binders.

📚 All Papers & Quick Reads

🗓️ Friday, Jan 23

• Comprehensive Molecular Docking and Molecular Dynamics Reveal Inhibitors of HER2 L755S, T798I, and T798M based on a Large Database of Curcumin Derivatives.: This study presents a methodology employing virtual screening to identify curcumin derivatives with selective affinity for the HER2 mutations L755S, T798I, and T798M. Curcumin derivatives were retrieved from the ChEMBL database and filtered using KNIME….
• Predicting the Mechanism of Action of Bawei Chufan Soup in Treating Teen Depression through Network Pharmacology, Molecular Docking and Molecular Dynamics Simulation.: Introduction The Bawei Chufan Soup (BWCFS) in Traditional Chinese Medicine (TCM) offers unique advantages in treating Teen Depression (TD). This study utilizes network pharmacology, molecular docking, and molecular dynamics simulations to predict the…
• In Silico Discovery of RIOK3 Inhibitors Against Pancreatic Ductal Adenocarcinoma Using Homology Modelling, Molecular Docking, Molecular Dynamics Simulations, ADMET Prediction, and MTT assay: Abstract Pancreatic ductal adenocarcinoma (PDAC) is an aggressive cancer strongly linked to RIO Kinase 3 (RIOK3), which promotes progression by stabilizing and phosphorylating Focal Adhesion Kinase (FAK). Advances in protein structure prediction,…
• Energy-Driven Innovations in Computational De Novo Protein Engineering.: Energy models play a crucial role in the advancement of computational de novo protein engineering, enabling the design of novel proteins with tailored functionalities. Proteins serve as the foundation of biochemical processes, making their precise…
• MetalloDock: Decoding Metalloprotein-Ligand Interactions via Physics-Aware Deep Learning for Metalloprotein Drug Discovery.: Accurate prediction of metalloprotein-ligand interactions is critical for metalloprotein-targeted drug discovery. Conventional docking tools and existing deep learning (DL) models fail to reliably capture metal-ligand interactions, hampering the discovery…
• Cytotoxicity, apoptosis, molecular docking, and molecular dynamics study of novel compounds of Sulfamide derivatives coupled with DHP scaffolds as potent inhibitors of the MCF-7, A549, SKOV-3, and EA. yh926 carcinoma cells.: A novel series of dihydropyridine-sulfonyl derivatives (AG-CHO and analogues A1-A7) were synthesized and structurally characterized. Molecular docking demonstrated favorable binding of these compounds to autophagy-associated and cancer-related targets,…
• Integrative gene target mapping, RNA sequencing, in silico molecular docking, ADMET profiling and molecular dynamics simulation study of marine derived molecules for type 1 diabetes mellitus.: Type 1 diabetes mellitus (T1DM) is a metabolic disease leading threat to human health around the world. Here we aimed to explore new biomarkers and potential therapeutic targets in T1DM through adopting integrated bioinformatics tools. The gene expression…
• AlphaFold for Docking Screens.: AlphaFold is an AI system developed by Google DeepMind to generate three-dimensional structures of proteins without experimental data. The models created with AlphaFold are available on the AlphaFold Protein Structure Database (AlphaFoldDB) (…

🛠️ Tools & Datasets

• 🛠 Tool: HHSuite - Remote homology detection with HMM-HMM comparison.
• 🛠 Tool: MAFFT - Multiple sequence alignment with high speed and accuracy.
• 💾 Dataset: SCOPe - Curated structural classification of proteins for fold analysis.
• 💾 Dataset: Pfam - Protein families database with curated multiple sequence alignments.

🤖 AI in Research Recap

• D4RT: Unified, Fast 4D Scene Reconstruction & Tracking - Google DeepMind: D4RT: Unified, Fast 4D Scene Reconstruction & Tracking    Google DeepMind
• The enzyme that doesn’t act like one: NUDT5 controls DNA building block production through structure, not catalysis - MSN: The enzyme that doesn’t act like one: NUDT5 controls DNA building block production through structure, not catalysis    MSN

🏢 Industry & Real-World Applications

• From Lab Bench to Breakthrough: How a UT Mentor-Student Partnership Sparked a Rising East Tennessee Biotech Company - UTHSC News: From Lab Bench to Breakthrough: How a UT Mentor-Student Partnership Sparked a Rising East Tennessee Biotech Company    UTHSC News
• USA–Saudi Biotech Alliance Advances Global Immune Medicine - Oncodaily: USA–Saudi Biotech Alliance Advances Global Immune Medicine    Oncodaily
• INTENT Biologics Receives FDA Agreement Granting a Full Waiver for its Pediatric Study Plan for PEP Biologic™ in Advanced Wound Care - Business Wire: INTENT Biologics Receives FDA Agreement Granting a Full Waiver for its Pediatric Study Plan for PEP Biologic™ in Advanced Wound Care    Business Wire
• A ‘lightbulb moment’: AI-designed intrabody probes track activity inside living cells - BioTechniques: A ‘lightbulb moment’: AI-designed intrabody probes track activity inside living cells    BioTechniques
• AAX Biotech and Vascurie announce new neuro-oncology collaboration - PharmaTimes: AAX Biotech and Vascurie announce new neuro-oncology collaboration    PharmaTimes
• Immunology biotech Agomab, eye-focused SpyGlass are latest biotechs to share IPO ambitions - Fierce Biotech: Immunology biotech Agomab, eye-focused SpyGlass are latest biotechs to share IPO ambitions    Fierce Biotech
• 2026: the year AI stops being optional in drug discovery - Drug Target Review: 2026: the year AI stops being optional in drug discovery    Drug Target Review

💼 Jobs & Opportunities

• Retraction Note: Antibodies against endogenous retroviruses promote lung cancer immunotherapy - Nature (Nature Careers)
• Atmospheric deposition enhances marine methane production and emissions from global oceans - Nature (Nature Careers)

📅 Events

• Structural Biology Events
• Protein Design Hub (LinkedIn Group)

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