Recep Adiyaman
Weekly Digest February 06, 2026 · 21 min read

Weekly Digest: Feb 02 - Feb 06, 2026

A curated summary of the top protein engineering and structure prediction signals from Feb 02 - Feb 06, 2026.

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Daily curated signals from arXiv, PubMed, and BioRxiv.

🧬 Weekly Recap

Feb 02 - Feb 06, 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

🗓️ Monday, Feb 02

Evaluating zero-shot prediction of monomeric protein design success by AlphaFold, ESMFold, and ProteinMPNN.

🧬 Abstract

De novo protein design has enabled the creation of proteins with diverse functionalities that are not found in nature. Despite recent advances, experimental success rates remain inconsistent and context-dependent, posing a bottleneck for broader applications of de novo design. To overcome this, structure and sequence prediction models have been applied to assess design quality prior to experimental testing to save time and resources. In this study, we examined the extent to which AlphaFold, Protein MPNN, and ESMFold can discriminate between experimentally successful and unsuccessful designs. We first curated a benchmark dataset of 614 experimentally characterized de novo designed monomers from 11 different design studies between 2012 and 2021. All predictive models demonstrated moderate ability to discriminate experimental successes (expressed, soluble, monomeric, and fold with the correct secondary structure) from failures. Still, many failed designs have better confidence metrics than successful designs, and confidence metrics were topology-dependent. Among all computational models evaluated, ESMFold average predicted local-distance difference test (pLDDT) yielded the best individual performance at distinguishing between successful and unsuccessful designs. A logistic regression model combining all confidence metrics provided only modest improvement over ESMFold pLDDT alone. Overall, these results show that these models can serve as an initial filtering strategy prior to experimental validation; however, their utility at accurately predicting experimentally successful designs remains limited without task-specific training.

Why it matters: Critical for improving fold accuracy and reducing structural uncertainty in de novo design.

🗓️ Tuesday, Feb 03

Comparison of In Vitro Multiple Physiological Activities of Cys-Tyr-Gly-Ser-Arg (CYGSR) Linear and Cyclic Peptides and Analysis Based on Molecular Docking.

🧬 Abstract

Peptide cyclization is a strategy to improve biological stability and functional activity, but direct comparison between linear and cyclic peptides with the same sequence is still limited. In this study, linear (L-CR5) and cyclic (C-CR5) forms were synthesized, and biological functions such as antioxidant, whitening, and anti-wrinkle activity were compared and evaluated. C-CR5 showed about 22.3 times of DPPH radical scavenging activity, which was significantly stronger than L-CR5, and tyrosinase inhibition increased rapidly in C-CR5 to reach inhibition of 95% or more, whereas L-CR5 showed only moderate activity in the same range (about 6.5 times). MMP-1 expression in the evaluation of anti-wrinkle activity did not show a decreasing trend in L-CR5 at all, while C-CR5 showed an anti-wrinkle effect, which was reduced by about 92.8% at 400 μg/mL. As a result of molecular docking analysis, C-CR5 exhibited lower MolDock scores than L-CR5 toward both tyrosinase and MMP-1, indicating a potentially higher binding affinity and improved binding stability. This is expected to be due to reduced structural flexibility and optimized residue directions (especially Tyr and Arg). These results indicate that peptide cyclization is an example of enhanced functional bioactivity of CYGSR and provides a positive case for the structure-activity relationship.

Why it matters: Enhances small-molecule or peptide docking accuracy for targeted drug discovery.

🗓️ Wednesday, Feb 04

Decrypting potential mechanisms linking ochratoxin A to hepatocellular carcinoma: an integrated approach combining toxicology, machine learning, molecular docking, and molecular dynamics simulation.

🧬 Abstract

Background Ochratoxin A (OTA), a common food-borne mycotoxin, is a potential human carcinogen, yet the specific molecular mechanisms linking it to hepatocellular carcinoma (HCC) remain unclear. Methods We integrated network toxicology to predict OTA targets and intersected them with HCC transcriptomic data to identify key candidate genes. Functional enrichment analysis was then conducted. Multiple machine learning algorithms were applied to screen and validate core genes. Furthermore, molecular docking and molecular dynamics (MD) simulations were employed to evaluate the binding stability between OTA and key target proteins. Results A total of 50 key genes were identified as potential targets for potential OTA-associated hepatocarcinogenesis. Enrichment analysis revealed their significant involvement in critical processes such as xenobiotic metabolism and oxidative stress response. Machine learning analysis prioritized eight core genes (AURKA, GABARAPL1, CA2, PARP1, LMNA, SLC27A5, EPHX2, and GSTP1), and a combined diagnostic model demonstrated outstanding performance (AUC = 0.986). Structural analyses via molecular docking and MD simulations confirmed stable binding interactions between OTA and these core targets. Conclusions This integrated computational study identifies a set of candidate genes through which OTA may potentially interact with HCC-associated molecular networks. The robust binding predicted between OTA and the core targets provides a structural basis for these interactions. These findings offer a prioritized list of targets and a theoretical framework for subsequent experimental validation and investigation into OTA’s toxicological role in HCC.

Why it matters: Enhances small-molecule or peptide docking accuracy for targeted drug discovery.

🗓️ Thursday, Feb 05

High-accuracy protein complex structure modeling based on sequence-derived structure complementarity.

🧬 Abstract

In living organisms, proteins perform key functions required for life activities by interacting to form complexes. Determining the protein complex structure is crucial for understanding and mastering biological functions. Although AlphaFold2 makes a revolutionary breakthrough in predicting protein monomeric structures, accurately capturing inter-chain interaction signals and modeling the structures of protein complexes remain a formidable challenge. In this work, we report DeepSCFold, a pipeline for improving protein complex structure modeling. DeepSCFold uses sequence-based deep learning models to predict protein-protein structural similarity and interaction probability, providing a foundation for identifying interaction partners and constructing deep paired multiple-sequence alignments (MSAs) for protein complex structure prediction. Benchmark results show that DeepSCFold significantly increases the accuracy of protein complex structure prediction compared with state-of-the-art methods. For multimer targets from CASP15, DeepSCFold achieves an improvement of 11.6% and 10.3% in TM-score compared to AlphaFold-Multimer and AlphaFold3, respectively. Furthermore, when applied to antibody-antigen complexes from the SAbDab database, DeepSCFold enhances the prediction success rate for antibody-antigen binding interfaces by 24.7% and 12.4% over AlphaFold-Multimer and AlphaFold3, respectively. These results demonstrate that DeepSCFold effectively captures intrinsic and conserved protein-protein interaction patterns through sequence-derived structure-aware information, rather than relying solely on sequence-level co-evolutionary signals.

🗓️ Friday, Feb 06

A New Insight into the Study of Neural Cell Adhesion Molecule (NCAM) Polysialylation Inhibition Incorporated the Molecular Docking Models into the NMR Spectroscopy of a Crucial Peptide-Ligand Interaction.

🧬 Abstract

The expression of polysialic acid (polySia) on the neuronal cell adhesion molecule (NCAM) is called NCAM-polysialylation, which is strongly related to the migration and invasion of tumor cells and aggressive clinical status. During the NCAM polysialylation process, polysialyltransferases (polySTs), such as polysialyltransferase IV (ST8SIA4) or polysialyltransferase II (ST8SIA2), can catalyze the addition of CMP-sialic acid (CMP-Sia) to the NCAM to form polysialic acid (polySia). In this study, the docking models of polysialyltransferase IV (ST8Sia4) protein and different ligands were predicted using Alphafold 3 and DiffDock servers, and the prediction accuracy was further verified using the NMR experimental spectra of the interactions between polysialyltransferase domain (PSTD), a crucial peptide domain in ST8Sia4, and a different ligand. This combination strategy provides new insights into a quick and effective screening for inhibitors of tumor cell migration.

Why it matters: Enhances small-molecule or peptide docking accuracy for targeted drug discovery.


📚 All Papers & Quick Reads

🗓️ Monday, Feb 02

🗓️ Tuesday, Feb 03

🗓️ Wednesday, Feb 04

🗓️ Thursday, Feb 05

🗓️ Friday, Feb 06


🛠️ Tools & Datasets

  • 🛠 Tool: MultiFOLD/IntFOLD - High-performance protein structure prediction and quality assessment server.
  • 🛠 Tool: PyMOL - Gold standard for molecular visualization and publication-quality imaging.
  • 💾 Dataset: AlphaFold Structure Database - 200M+ predicted structures from DeepMind/EMBL-EBI.
  • 💾 Dataset: Uniprot Knowledgebase - The world’s most comprehensive resource for protein sequence and annotation.
  • 🛠 Tool: Chai-1 - Multi-modal foundation model for molecular structure prediction.
  • 💾 Dataset: PDB-REDO - Optimized protein structure database with refined models.
  • 🛠 Tool: Boltz-1 - Open-source biomolecular structure prediction model.
  • 💾 Dataset: CATH - Hierarchical protein domain classification for structure and function.
  • 🛠 Tool: ProteinSolver - Graph-based neural network for protein sequence design.
  • 💾 Dataset: SCOPe - Curated structural classification of proteins for fold analysis.
  • 🛠 Tool: RFdiffusion - State-of-the-art generative model for de novo protein design.
  • 💾 Dataset: Pfam - Protein families database with curated multiple sequence alignments.

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