Protein Design Digest

Issue #128: Prediction of Antibody Non-Specificity using Protein Language Models and Biophysical Parameters

Protein Design Digest #128: Computational Assessment of Phytochemical Inhibitors of Cytochrome P450 …

Issue #127: BA-Pred and RMSD-Pred: Integrated Graph Neural Network Models for Accurate Protein-Ligand Binding Affinity and Binding Pose Prediction.

Protein Design Digest #127: BA-Pred and RMSD-Pred: Integrated Graph Neural Network Models for Accura…

Issue #126: Defining Active Conformations from Substrate-Bound Structures Enables Active-State AlphaFold2 Modeling of All 437 Human Catalytic Protein Kinase Domains.

Protein Design Digest #126: BA-Pred and RMSD-Pred: Integrated Graph Neural Network Models for Accura…

Issue #125: Decoding the Grammar of Protein–Protein Interaction Interfaces with Multimodal Representations

Protein Design Digest #125: BA-Pred and RMSD-Pred: Integrated Graph Neural Network Models for Accura…

Weekly Digest: Jun 01 - Jun 05, 2026

A curated summary of the top protein engineering and structure prediction signals from Jun 01 - Jun 05, 2026.

Issue #124: Unveiling the Potential Therapeutic Efficacy of Gold Ceria Nanohybrid as an Anticancer Agent: A Special Insight to Molecular Docking Study.

Protein Design Digest #124: Computational Assessment of Phytochemical Inhibitors of Cytochrome P450 …

Issue #123: Identification and Characterization of New Therapeutic Candidates for Naegleria fowleri- brain-eating Amoeba: A Multi-target Approach Based on 3D-QSAR, Molecular Docking, MM-GBSA, ADMET and Molecular Dynamics.

Protein Design Digest #123: Computational Assessment of Phytochemical Inhibitors of Cytochrome P450 …

Issue #122: Analysis of toxicity and mechanism of xylazine on testis with network toxicology and molecular docking strategy.

Protein Design Digest #122: Tocotrienol as a multi-target inhibitor of ICAM-1, VCAM-1, and E-selecti…

Issue #121: AI-driven drug-target interaction prediction: current progress, challenges, and future roadmap for precision medicine.

Protein Design Digest #121: Tocotrienol as a multi-target inhibitor of ICAM-1, VCAM-1, and E-selecti…

Issue #120: Adversarial Sequence Mutations in AlphaFold and ESMFold Reveal Nonphysical Structural Invariance, Confidence Failures, and Concerns for Protein Design

Protein Design Digest #120: Adversarial Sequence Mutations in AlphaFold and ESMFold Reveal Nonphysic…

Weekly Digest: May 25 - May 29, 2026

A curated summary of the top protein engineering and structure prediction signals from May 25 - May 29, 2026.

Issue #119: Integrating glycosylation in <i>de novo</i> protein design with ReGlyco Binder Design Filter

Protein Design Digest #119: Integrating glycosylation in <i>de novo</i> protein design with ReGlyc…

Issue #118: Computational Identification of Novel Inhibitors Targeting Multiple Proteins of Tomato Brown Rugose Fruit Virus (ToBRFV) Through AlphaFold-Based Protein Modeling, Molecular Docking, MM/GBSA Binding Free Energy Analysis, and Molecular Dynamics Simulation

Protein Design Digest #118: Computational Identification of Novel Inhibitors Targeting Multiple Prot…

Issue #117: Assessment of Alphafold Protein Models for Small-Molecule Ligand Docking versus Co-Folding.

Protein Design Digest #117: Assessment of Alphafold Protein Models for Small-Molecule Ligand Docking…

Issue #116: Exploring the immunomodulatory mechanisms of Astragalus membranaceus in esophageal cancer treatment through network pharmacology, molecular docking, and molecular dynamics simulation.

Protein Design Digest #116: Exploring the immunomodulatory mechanisms of Astragalus membranaceus in …

Issue #115: Integrative structural and physicochemical characterization of chalcone synthase enzymes from medicinal plants using AlphaFold, molecular docking, and molecular dynamics.

Protein Design Digest #115: Integrative structural and physicochemical characterization of chalcone …

Weekly Digest: May 18 - May 22, 2026

A curated summary of the top protein engineering and structure prediction signals from May 18 - May 22, 2026.

Issue #114: Benchmarking generative scaffold design methods for peptide engineering in TCR-MHC complexes

Protein Design Digest #114: Benchmarking generative scaffold design methods for peptide engineering …

Issue #113: High-Affinity Protein Binder Design via Flow Matching and In Silico Maturation

Protein Design Digest #113: Exploring the mechanism of saffron in treating viral myocarditis using n…

Issue #112: PlantP450Dock: an Automated Molecular Docking Pipeline of Plant Cytochrome P450s

Protein Design Digest #112: PlantP450Dock: an Automated Molecular Docking Pipeline of Plant Cytochro…

Issue #111: Toward Accurate RNA Folding Thermodynamics: Evaluation of Enhanced Sampling Methods for Force Field Benchmarking

Protein Design Digest #111: Toward Accurate RNA Folding Thermodynamics: Evaluation of Enhanced Sampl…

Issue #110: 3D-QSAR, Molecular Docking, Molecular Dynamics Simulation, and Pharmacokinetic Prediction of 1H-Pyrazolo[3,4-d]pyrimidine Derivatives as PI3Kδ Inhibitors.

Protein Design Digest #110: 3D-QSAR, Molecular Docking, Molecular Dynamics Simulation, and Pharmacok…

Weekly Digest: May 11 - May 15, 2026

A curated summary of the top protein engineering and structure prediction signals from May 11 - May 15, 2026.

Issue #109: AlphaFold and the Transformation of Structural Biology: Evolution, Applications, Limitations, and Future Directions

Protein Design Digest #109: AlphaFold and the Transformation of Structural Biology: Evolution, Appli…

Issue #108: scDock: streamlining drug discovery targeting cell-cell communication via scRNA-seq analysis and molecular docking.

Protein Design Digest #108: scDock: streamlining drug discovery targeting cell-cell communication vi…

Issue #107: Simulated construction of tilmicosin nucleic acid aptamers based on molecular docking and molecular dynamics techniques.

Protein Design Digest #107: Simulated construction of tilmicosin nucleic acid aptamers based on mole…

Issue #106: Protocol for analyzing potential targets of environmental pollutants in human diseases using network toxicology and molecular docking.

Protein Design Digest #106: scDock: streamlining drug discovery targeting cell-cell communication vi…

Issue #105: Efficient Adaptation of Structure-Aware Protein Language Models for Diverse Protein Applications.

Protein Design Digest #105: scDock: streamlining drug discovery targeting cell-cell communication vi…

Weekly Digest: May 04 - May 08, 2026

A curated summary of the top protein engineering and structure prediction signals from May 04 - May 08, 2026.

Issue #104: Identification of paucinervin D as a natural sphingosine-1-phosphate receptor 1 agonist: Insights from pharmacophore modeling, docking, molecular dynamics simulations, and density functional theory.

Protein Design Digest #104: Identification of paucinervin D as a natural sphingosine-1-phosphate rec…

Issue #103: Discovery of potent ALK tyrosine kinase inhibitors for thyroid cancer via machine learning modeling, molecular docking, MD simulations, and DFT study.

Protein Design Digest #103: Discovery of potent ALK tyrosine kinase inhibitors for thyroid cancer vi…

Issue #102: Advances in Molecular Docking Methodologies

Protein Design Digest #102: Advances in Molecular Docking Methodologies

Issue #101: Investigation of the potential mechanism by which methylparaben induces psoriasis: an integrated study using network toxicology, molecular docking, molecular dynamics simulation, and eight machine learning algorithms.

Protein Design Digest #101: Investigation of the potential mechanism by which methylparaben induces …

Issue #100: Exploring quantum frontiers in protein structure prediction: techniques, challenges, and opportunities.

Protein Design Digest #100: Exploring quantum frontiers in protein structure prediction: techniques,…

Weekly Digest: Apr 27 - May 01, 2026

A curated summary of the top protein engineering and structure prediction signals from Apr 27 - May 01, 2026.

Issue #99: The past, present and future of de novo protein design.

Protein Design Digest #99: The past, present and future of de novo protein design.

Issue #98: The Influence of Ligands on AlphaFold3 Prediction of Cryptic Pockets

Protein Design Digest #98: Identification of paucinervin D as a natural sphingosine-1-phosphate rec…

Issue #97: Enhancing CYP450-Ligand Binding Predictions: A Comparative Analysis of Ligand-Based and Hybrid Machine Learning Models.

Protein Design Digest #97: Enhancing CYP450-Ligand Binding Predictions: A Comparative Analysis of L…

Issue #96: Predicting the Mechanism of Action of Bawei Chufan Soup in Treating Teen Depression through Network Pharmacology, Molecular Docking and Molecular Dynamics Simulation.

Protein Design Digest #96: Predicting the Mechanism of Action of Bawei Chufan Soup in Treating Teen…

Issue #95: The transformative impact of AI-enabled AlphaFold 3: evolution, current status, and future prospects in structural biology.

Protein Design Digest #95: The transformative impact of AI-enabled AlphaFold 3: evolution, current …

Weekly Digest: Apr 20 - Apr 24, 2026

A curated summary of the top protein engineering and structure prediction signals from Apr 20 - Apr 24, 2026.

Issue #94: Comprehensive Molecular Docking and Molecular Dynamics Reveal Inhibitors of HER2 L755S, T798I, and T798M based on a Large Database of Curcumin Derivatives.

Protein Design Digest #94: Comprehensive Molecular Docking and Molecular Dynamics Reveal Inhibitors…

Issue #93: NNDock2: A neural network-based scoring function for ranking protein-protein docking models.

Protein Design Digest #93: NNDock2: A neural network-based scoring function for ranking protein-pro…

Issue #92: Advancing protein engineering via organic chemistry.

Protein Design Digest #92: Comprehensive Molecular Docking and Molecular Dynamics Reveal Inhibitors…

Weekly Digest: Apr 13 - Apr 17, 2026

A curated summary of the top protein engineering and structure prediction signals from Apr 13 - Apr 17, 2026.

Issue #91: From Atoms to Fragments: A Coarse Representation for Efficient and Functional Protein Design.

Protein Design Digest #91: Comprehensive Molecular Docking and Molecular Dynamics Reveal Inhibitors…

Issue #90: Evaluating zero-shot prediction of monomeric protein design success by AlphaFold, ESMFold, and ProteinMPNN.

Protein Design Digest #90: Evaluating zero-shot prediction of monomeric protein design success by A…

Issue #89: Binding Affinity and Interaction Profiles of Erinacines and Erinacerins with iNOS and NF-κB Revealed by Molecular Dynamics Simulations.

Protein Design Digest #89: Enhancing CYP450-Ligand Binding Predictions: A Comparative Analysis of L…

Issue #88: Evaluation of protein-RNA Docking Web Servers for Template-Free Docking and Comparison with the AlphaFold Server.

Protein Design Digest #88: Evaluation of protein-RNA Docking Web Servers for Template-Free Docking …

Issue #87: De novo protein design: a transformative frontier in clinical protein applications.

Protein Design Digest #87: Enhancing CYP450-Ligand Binding Predictions: A Comparative Analysis of L…

Weekly Digest: Apr 06 - Apr 10, 2026

A curated summary of the top protein engineering and structure prediction signals from Apr 06 - Apr 10, 2026.

Issue #86: Geometric Properties of the Voronoi Tessellation in Latent Semantic Manifolds of Large Language Models

Protein Design Digest #86: Enhancing CYP450-Ligand Binding Predictions: A Comparative Analysis of L…

Issue #85: BA-Pred and RMSD-Pred: Integrated Graph Neural Network Models for Accurate Protein-Ligand Binding Affinity and Binding Pose Prediction.

Protein Design Digest #85: BA-Pred and RMSD-Pred: Integrated Graph Neural Network Models for Accura…

Issue #84: Salt Bridge Builder: Using Residue Distances to Predict Salt Bridge Formation.

Protein Design Digest #84: BA-Pred and RMSD-Pred: Integrated Graph Neural Network Models for Accura…

Issue #83: Quantum chemical, spectroscopic, molecular docking, molecular dynamics analyses and ADMET properties: Nifedipine.

Protein Design Digest #83: BA-Pred and RMSD-Pred: Integrated Graph Neural Network Models for Accura…

Weekly Digest: Mar 30 - Apr 03, 2026

A curated summary of the top protein engineering and structure prediction signals from Mar 30 - Apr 03, 2026.

Issue #82: AlphaFold for Docking Screens.

Protein Design Digest #82: BA-Pred and RMSD-Pred: Integrated Graph Neural Network Models for Accura…

Issue #81: Molecular Dynamics Simulations: Principles, Algorithms, and Emerging Applications

Protein Design Digest #81: BA-Pred and RMSD-Pred: Integrated Graph Neural Network Models for Accura…

Issue #80: A Mini Review on Metal Complexes as Potential Anti-SARS-CoV-2 Agents: Insights from Molecular Docking Studies.

Protein Design Digest #80: Enhancing CYP450-Ligand Binding Predictions: A Comparative Analysis of L…

Issue #79: TurboESM: Ultra-Efficient 3-Bit KV Cache Quantization for Protein Language Models with Orthogonal Rotation and QJL Correction

Protein Design Digest - 2026-03-31 - Enhancing CYP450-Ligand Binding Predictions: A Comparative Analysis of Ligand-Based and Hybrid Machine Learning Models.

Issue #78: FastMDAnalysis: Software for Automated Analysis of Molecular Dynamics Trajectories.

Protein Design Digest - 2026-03-30 - Enhancing CYP450-Ligand Binding Predictions: A Comparative Analysis of Ligand-Based and Hybrid Machine Learning Models.

Weekly Digest: Mar 23 - Mar 27, 2026

A curated summary of the top protein engineering and structure prediction signals from Mar 23 - Mar 27, 2026.

Issue #77: Computational Identification of Novel Inhibitors Targeting Multiple Proteins of Tomato Brown Rugose Fruit Virus (ToBRFV) Through AlphaFold-Based Protein Modeling, Molecular Docking, MM/GBSA Binding Free Energy Analysis, and Molecular Dynamics Simulation

Protein Design Digest - 2026-03-27 - Computational Identification of Novel Inhibitors Targeting Multiple Proteins of Tomato Brown Rugose Fruit Virus (ToBRFV) Through AlphaFold-Based Protein Modeling, Molecular Docking, MM/GBSA Binding Free Energy Analysis, and Molecular Dynamics Simulation

Issue #76: DynaBench: Dynamic data for the docking benchmark.

Protein Design Digest - 2026-03-26 - DynaBench: Dynamic data for the docking benchmark.

Issue #75: Integrative structural and physicochemical characterization of chalcone synthase enzymes from medicinal plants using AlphaFold, molecular docking, and molecular dynamics.

Protein Design Digest - 2026-03-25 - Integrative structural and physicochemical characterization of chalcone synthase enzymes from medicinal plants using AlphaFold, molecular docking, and molecular dynamics.

Issue #74: Best Practices in Mixed-Solvent Molecular Dynamics and Solvent-Site-Biased Docking.

Protein Design Digest - 2026-03-24 - Enhancing CYP450-Ligand Binding Predictions: A Comparative Analysis of Ligand-Based and Hybrid Machine Learning Models.

Issue #73: AlphaFold3: A Transformer in Life Sciences.

Protein Design Digest - 2026-03-23 - Enhancing CYP450-Ligand Binding Predictions: A Comparative Analysis of Ligand-Based and Hybrid Machine Learning Models.

Weekly Digest: Mar 16 - Mar 20, 2026

A curated summary of the top protein engineering and structure prediction signals from Mar 16 - Mar 20, 2026.

Issue #72: Design, Synthesis, Molecular Docking, and Biological Evaluation of Tanshinone IIA Derivatives as Antibreast Cancer Agents.

Protein Design Digest - 2026-03-20 - Mechanisms of Okanin against wound healing based on network pharmacology, molecular docking and molecular dynamics simulation.

Issue #71: Design, Synthesis, Molecular Dynamics Simulations, and Biological Evaluation of PB2 Inhibitors as Anti-Influenza A Virus Agent.

Protein Design Digest - 2026-03-19 - Mechanisms of Okanin against wound healing based on network pharmacology, molecular docking and molecular dynamics simulation.

Issue #70: Molecular Dynamics-Guided Design and Chemoproteomic Profiling of Covalent Kinase Activity Probes.

Protein Design Digest - 2026-03-18 - Mechanisms of Okanin against wound healing based on network pharmacology, molecular docking and molecular dynamics simulation.

Issue #69: Molecular embedding-based algorithm selection in protein-ligand docking.

Protein Design Digest - 2026-03-17 - Molecular embedding-based algorithm selection in protein-ligand docking.

Issue #68: Advantages and Limitations of AlphaFold in Structural Biology: Insights from Recent Studies.

Protein Design Digest - 2026-03-16 - Advantages and Limitations of AlphaFold in Structural Biology: Insights from Recent Studies.

Weekly Digest: Mar 09 - Mar 13, 2026

A curated summary of the top protein engineering and structure prediction signals from Mar 09 - Mar 13, 2026.

Issue #67: How to make the most of your masked language model for protein engineering

Protein Design Digest - 2026-03-13 - Discovery of a Hematopoietic Manifold in scGPT Yields a Method for Extracting Performant Algorithms from Biological Foundation Model Internals

Issue #66: A multimodal approach integrating spectroscopy, deep learning guided molecular docking, and molecular dynamics simulation for predictive assessment of pioglitazone to albumin binding for formulation development.

Protein Design Digest - 2026-03-12 - A multimodal approach integrating spectroscopy, deep learning guided molecular docking, and molecular dynamics simulation for predictive assessment of pioglitazone to albumin binding for formulation development.

Issue #65: Multispectral, Molecular Docking, and Dynamics Simulation Studies of Secalonic Acid F Binding to Human Serum Albumin.

Protein Design Digest - 2026-03-11 - A multimodal approach integrating spectroscopy, deep learning guided molecular docking, and molecular dynamics simulation for predictive assessment of pioglitazone to albumin binding for formulation development.

Issue #64: scDock: Streamlining drug discovery targeting cell-cell communication via scRNA-seq analysis and molecular docking.

Protein Design Digest - 2026-03-10 - scDock: Streamlining drug discovery targeting cell-cell communication via scRNA-seq analysis and molecular docking.

Issue #63: MutPPI+: a multimodal framework for predicting mutation effects on protein-protein interactions via mutation-path-based data augmentation.

Protein Design Digest - 2026-03-09 - scDock: Streamlining drug discovery targeting cell-cell communication via scRNA-seq analysis and molecular docking.

Weekly Digest: Mar 02 - Mar 06, 2026

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

Issue #62: Identification of Bioactive Ingredients and Mechanistic Pathways of Xuefu Zhuyu Decoction in Ventricular Remodeling: A Network Pharmacology, Molecular Docking and Molecular Dynamics Simulations.

Protein Design Digest - 2026-03-06 - Identification of Bioactive Ingredients and Mechanistic Pathways of Xuefu Zhuyu Decoction in Ventricular Remodeling: A Network Pharmacology, Molecular Docking and Molecular Dynamics Simulations.

Issue #61: Investigation of the potential mechanism by which methylparaben induces psoriasis: an integrated study using network toxicology, molecular docking, molecular dynamics simulation, and eight machine learning algorithms.

Protein Design Digest - 2026-03-05 - Investigation of the potential mechanism by which methylparaben induces psoriasis: an integrated study using network toxicology, molecular docking, molecular dynamics simulation, and eight machine learning algorithms.

Issue #60: Anomalous Effect of Denaturant on Protein Unfolding Dynamics Revealed by Single Molecule Manipulation Experiments.

Protein Design Digest - 2026-03-04 - Investigation of the potential mechanism by which methylparaben induces psoriasis: an integrated study using network toxicology, molecular docking, molecular dynamics simulation, and eight machine learning algorithms.

Issue #59: Development of DHODH inhibitors incorporating virtual screening, pharmacophore modeling, fragment-based optimization methods, ADMET, molecular docking, molecular dynamics, PCA analysis, and free energy landscape.

Protein Design Digest - 2026-03-03 - Development of DHODH inhibitors incorporating virtual screening, pharmacophore modeling, fragment-based optimization methods, ADMET, molecular docking, molecular dynamics, PCA analysis, and free energy landscape.

Issue #58: Hybrid Computational Framework Integrating Ensemble Learning, Molecular Docking, and Dynamics for Predicting Antimalarial Efficacy of Malaria Box Compounds.

Protein Design Digest - 2026-03-02 - Development of DHODH inhibitors incorporating virtual screening, pharmacophore modeling, fragment-based optimization methods, ADMET, molecular docking, molecular dynamics, PCA analysis, and free energy landscape.

Weekly Digest: Feb 23 - Feb 27, 2026

A curated summary of the top protein engineering and structure prediction signals from Feb 23 - Feb 27, 2026.

Issue #57: Discovery of potent ALK tyrosine kinase inhibitors for thyroid cancer via machine learning modeling, molecular docking, MD simulations, and DFT study.

Protein Design Digest - 2026-02-27 - Discovery of potent ALK tyrosine kinase inhibitors for thyroid cancer via machine learning modeling, molecular docking, MD simulations, and DFT study.

Issue #56: A Neural Time-Series Learning Method for Accelerating Free-Energy Perturbation and Rare-Event Molecular Dynamics Simulations.

Protein Design Digest - 2026-02-26 - Discovery of potent ALK tyrosine kinase inhibitors for thyroid cancer via machine learning modeling, molecular docking, MD simulations, and DFT study.

Issue #55: ManCAR: Manifold-Constrained Latent Reasoning with Adaptive Test-Time Computation for Sequential Recommendation

Protein Design Digest - 2026-02-25 - Discovery of potent ALK tyrosine kinase inhibitors for thyroid cancer via machine learning modeling, molecular docking, MD simulations, and DFT study.

Issue #54: Self-Aware Object Detection via Degradation Manifolds

Protein Design Digest - 2026-02-24 - Discovery of potent ALK tyrosine kinase inhibitors for thyroid cancer via machine learning modeling, molecular docking, MD simulations, and DFT study.

Issue #53: Predicting the active sites of quinolone antibiotics interacting with organisms by deep learning and molecular docking.

Protein Design Digest - 2026-02-23 - Discovery of potent ALK tyrosine kinase inhibitors for thyroid cancer via machine learning modeling, molecular docking, MD simulations, and DFT study.

Weekly Digest: Feb 16 - Feb 20, 2026

A curated summary of the top protein engineering and structure prediction signals from Feb 16 - Feb 20, 2026.

Issue #52: 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.

Protein Design Digest - 2026-02-20 - 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.

Issue #51: Structure-Guided Engineering of High-Affinity Antibodies Against Zika Virus Using Deep Learning and Molecular Dynamics.

Protein Design Digest - 2026-02-19 - 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.

Issue #50: Molecular docking: a computational approach for the discovery of novel targets against visceral leishmaniasis.

Protein Design Digest - 2026-02-18 - 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.

Issue #49: AlphaFold2-Guided Cyclic Peptide Stabilizer Design to Target Protein-Protein Interactions.

Protein Design Digest - 2026-02-17 - 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.

Issue #48: DeepFold-PLM: accelerating protein structure prediction via efficient homology search using protein language models.

Protein Design Digest - 2026-02-16 - DeepFold-PLM: accelerating protein structure prediction via efficient homology search using protein language models.

Weekly Digest: Feb 09 - Feb 13, 2026

A curated summary of the top protein engineering and structure prediction signals from Feb 09 - Feb 13, 2026.

Issue #47: Deconvolving mutation effects on protein stability and function with disentangled protein language models.

Protein Design Digest - 2026-02-13 - 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.

Issue #46: Unfreezing structural biology for drug discovery.

Protein Design Digest - 2026-02-12 - 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.

Issue #45: De novo protein design: a transformative frontier in clinical protein applications.

Protein Design Digest - 2026-02-11 - 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.

Issue #44: Immunoinformatics and molecular docking reveal potential multi-epitope vaccine against Pseudomonas aeruginosa.

Protein Design Digest - 2026-02-10 - 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.

Issue #43: From Atoms to Cells: AI-Based Structure Prediction Fueling Molecular Dynamics Simulations in Computational Structural Biology.

Protein Design Digest - 2026-02-09 - 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.

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.

Issue #42: De novo protein design enables targeting of intractable oncogenic interfaces

Protein Design Digest - 2026-02-06 - 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.

Issue #41: High-accuracy protein complex structure modeling based on sequence-derived structure complementarity.

Protein Design Digest - 2026-02-05 - 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.

Issue #40: Decrypting potential mechanisms linking ochratoxin A to hepatocellular carcinoma: an integrated approach combining toxicology, machine learning, molecular docking, and molecular dynamics simulation.

Protein Design Digest - 2026-02-04 - Decrypting potential mechanisms linking ochratoxin A to hepatocellular carcinoma: an integrated approach combining toxicology, machine learning, molecular docking, and molecular dynamics simulation.

Issue #39: Comparison of In Vitro Multiple Physiological Activities of Cys-Tyr-Gly-Ser-Arg (CYGSR) Linear and Cyclic Peptides and Analysis Based on Molecular Docking.

Protein Design Digest - 2026-02-03 - Comparison of In Vitro Multiple Physiological Activities of Cys-Tyr-Gly-Ser-Arg (CYGSR) Linear and Cyclic Peptides and Analysis Based on Molecular Docking.

Issue #38: Evaluating zero-shot prediction of monomeric protein design success by AlphaFold, ESMFold, and ProteinMPNN.

Protein Design Digest - 2026-02-02 - Evaluating zero-shot prediction of monomeric protein design success by AlphaFold, ESMFold, and ProteinMPNN.

Issue #37: Efficacy of Ipflufenoquin against Strawberry Gray Mold: Insights from AlphaFold- Based Structural Modeling and Genome-Wide Transcriptomic Analysis.

Protein Design Digest - 2026-01-31 - Efficacy of Ipflufenoquin against Strawberry Gray Mold: Insights from AlphaFold- Based Structural Modeling and Genome-Wide Transcriptomic Analysis.

Weekly Digest: Jan 26 - Jan 30, 2026

A curated summary of the top protein engineering and structure prediction signals from Jan 26 - Jan 30, 2026.

Issue #36: Scalable embedding fusion with protein language models: insights from benchmarking text-integrated representations.

Protein Design Digest - 2026-01-30 - Scalable embedding fusion with protein language models: insights from benchmarking text-integrated representations.

Issue #35: PepScorer::RMSD: An Improved Machine Learning Scoring Function for Protein-Peptide Docking.

Protein Design Digest - 2026-01-29 - PepScorer::RMSD: An Improved Machine Learning Scoring Function for Protein-Peptide Docking.

Issue #34: Tailored pyrrole-based imidazothiazole scaffolds: Synthetic elaboration, enzyme kinetic profiling and DFT-guided molecular docking toward Antidiabetic therapeutics.

Protein Design Digest - 2026-01-28 - Tailored pyrrole-based imidazothiazole scaffolds: Synthetic elaboration, enzyme kinetic profiling and DFT-guided molecular docking toward Antidiabetic therapeutics.

Issue #33: ModelCIF update: Supporting Emerging Classes of Computational Macromolecular Models.

Protein Design Digest - 2026-01-27 - ModelCIF update: Supporting Emerging Classes of Computational Macromolecular Models.

Issue #32: Energy-Driven Innovations in Computational De Novo Protein Engineering.

Protein Design Digest - 2026-01-26 - Energy-Driven Innovations in Computational De Novo Protein Engineering.

Issue #31: Comprehensive Molecular Docking and Molecular Dynamics Reveal Inhibitors of HER2 L755S, T798I, and T798M based on a Large Database of Curcumin Derivatives.

Protein Design Digest - 2026-01-25 - Comprehensive Molecular Docking and Molecular Dynamics Reveal Inhibitors of HER2 L755S, T798I, and T798M based on a Large Database of Curcumin Derivatives.

Issue #30: DynaBench: Dynamic data for the docking benchmark.

Protein Design Digest - 2026-01-24 - DynaBench: Dynamic data for the docking benchmark.

Weekly Digest: Jan 19 - Jan 23, 2026

A curated summary of the top protein engineering and structure prediction signals from Jan 19 - Jan 23, 2026.

Issue #29: Mechanistic Investigation of Astragalus Root in the Management of T2DM-NAFLD Comorbidity: An Integrated Network Pharmacology, Molecular Docking, Molecular Dynamics Simulation, and In Vitro Study

Protein Design Digest - 2026-01-23 - Mechanistic Investigation of Astragalus Root in the Management of T2DM-NAFLD Comorbidity: An Integrated Network Pharmacology, Molecular Docking, Molecular Dynamics Simulation, and In Vitro Study

Issue #28: Predicting the Mechanism of Action of Bawei Chufan Soup in Treating Teen Depression through Network Pharmacology, Molecular Docking and Molecular Dynamics Simulation.

Protein Design Digest - 2026-01-22 - Predicting the Mechanism of Action of Bawei Chufan Soup in Treating Teen Depression through Network Pharmacology, Molecular Docking and Molecular Dynamics Simulation.

Issue #27: AlphaFold can help African researchers to do cutting-edge structural biology.

Protein Design Digest - 2026-01-21 - Mechanistic Investigation of Astragalus Root in the Management of T2DM-NAFLD Comorbidity: An Integrated Network Pharmacology, Molecular Docking, Molecular Dynamics Simulation, and In Vitro Study

Issue #26: MetalloDock: Decoding Metalloprotein-Ligand Interactions via Physics-Aware Deep Learning for Metalloprotein Drug Discovery.

Protein Design Digest - 2026-01-20 - MetalloDock: Decoding Metalloprotein-Ligand Interactions via Physics-Aware Deep Learning for Metalloprotein Drug Discovery.

Issue #25: Enhancing CYP450-Ligand Binding Predictions: A Comparative Analysis of Ligand-Based and Hybrid Machine Learning Models.

Protein Design Digest - 2026-01-19 - Enhancing CYP450-Ligand Binding Predictions: A Comparative Analysis of Ligand-Based and Hybrid Machine Learning Models.

Weekly Digest: Jan 12 - Jan 16, 2026

A curated summary of the top protein engineering and structure prediction signals from Jan 12 - Jan 16, 2026.

Issue #24: In Silico Discovery of RIOK3 Inhibitors Against Pancreatic Ductal Adenocarcinoma Using Homology Modelling, Molecular Docking, Molecular Dynamics Simulations, ADMET Prediction, and MTT assay

Protein Design Digest - 2026-01-16 - In Silico Discovery of RIOK3 Inhibitors Against Pancreatic Ductal Adenocarcinoma Using Homology Modelling, Molecular Docking, Molecular Dynamics Simulations, ADMET Prediction, and MTT assay

Issue #23: Benchmarking co-folding methods to predict the structures of covalent protein-ligand complexes.

Protein Design Digest - 2026-01-15 - Benchmarking co-folding methods to predict the structures of covalent protein-ligand complexes.

Issue #22: Advantages and Limitations of AlphaFold in Structural Biology: Insights from Recent Studies.

Protein Design Digest - 2026-01-14 - Advantages and Limitations of AlphaFold in Structural Biology: Insights from Recent Studies.

Issue #21: Geometric deep learning assists protein engineering. Opportunities and Challenges.

Protein Design Digest - 2026-01-13 - Geometric deep learning assists protein engineering. Opportunities and Challenges.

Issue #20: Synthesis, Anticancer Evaluation, and Molecular Docking of Triazolylmethyl-Dihydroquinazolinyl Benzoate Derivatives as Potential PARP-1 Inhibitors.

Protein Design Digest - 2026-01-12 - Synthesis, Anticancer Evaluation, and Molecular Docking of Triazolylmethyl-Dihydroquinazolinyl Benzoate Derivatives as Potential PARP-1 Inhibitors.

Issue #19: Integrative Network Pharmacology and Molecular Docking-Based Validation of Berberine as a Therapeutic Agent in Arsenic-Induced Cardiotoxicity.

Protein Design Digest - 2026-01-11 - Integrative Network Pharmacology and Molecular Docking-Based Validation of Berberine as a Therapeutic Agent in Arsenic-Induced Cardiotoxicity.

Issue #18: Integrated QSAR, molecular docking, and dynamics-based discovery of a potent selective HDAC1 inhibitor with therapeutic potential in aggressive cancers.

Protein Design Digest - 2026-01-10 - Integrated QSAR, molecular docking, and dynamics-based discovery of a potent selective HDAC1 inhibitor with therapeutic potential in aggressive cancers.

Weekly Digest: Jan 05 - Jan 09, 2026

A curated summary of the top protein engineering and structure prediction signals from Jan 05 - Jan 09, 2026.

Issue #17: Discovery of PPARγ Partial Agonists for Treatment of Type 2 Diabetes Based on an Integrated Virtual Screening Strategy that Combines Fragment Molecular Orbital Calculations, Machine Learning, Molecular Docking, Interaction Fingerprint Filtering, and Molecular Dynamics Simulations.

Protein Design Digest - 2026-01-09 - Discovery of PPARγ Partial Agonists for Treatment of Type 2 Diabetes Based on an Integrated Virtual Screening Strategy that Combines Fragment Molecular Orbital Calculations, Machine Learning, Molecular Docking, Interaction Fingerprint Filtering, and Molecular Dynamics Simulations.

Issue #16: Discovery of PPARγ Partial Agonists for Treatment of Type 2 Diabetes Based on an Integrated Virtual Screening Strategy that Combines Fragment Molecular Orbital Calculations, Machine Learning, Molecular Docking, Interaction Fingerprint Filtering, and Molecular Dynamics Simulations.

Protein Design Digest - 2026-01-08 - Discovery of PPARγ Partial Agonists for Treatment of Type 2 Diabetes Based on an Integrated Virtual Screening Strategy that Combines Fragment Molecular Orbital Calculations, Machine Learning, Molecular Docking, Interaction Fingerprint Filtering, and Molecular Dynamics Simulations.

Issue #15: SMARTDock: A Toolkit for the Automated Development of Target-Specific Scoring Functions Using Bioactivity Data.

Protein Design Digest - 2026-01-07 - Discovery of PPARγ Partial Agonists for Treatment of Type 2 Diabetes Based on an Integrated Virtual Screening Strategy that Combines Fragment Molecular Orbital Calculations, Machine Learning, Molecular Docking, Interaction Fingerprint Filtering, and Molecular Dynamics Simulations.

Issue #1: Discovery of PPARγ Partial Agonists for Treatment of Type 2 Diabetes Based on an Integrated Virtual Screening Strategy that Combines Fragment Molecular Orbital Calculations, Machine Learning, Molecular Docking, Interaction Fingerprint Filtering, and Molecular Dynamics Simulations.

Issue #1: AlphaFold for Docking Screens.

Protein Design Digest - 2026-01-06 - AlphaFold for Docking Screens.

Issue #14: Assessing the validity of leucine zipper constructs predicted by AlphaFold.

Protein Design Digest - 2026-01-05 - AlphaFold for Docking Screens.

Issue #13: AlphaFold for Docking Screens.

Protein Design Digest - 2026-01-05 - AlphaFold for Docking Screens.

Issue #1: AlphaFold for Docking Screens.

Protein Design Digest - 2026-01-05 - AlphaFold for Docking Screens.

Weekly Digest: Dec 28 - Jan 04, 2026

A curated summary of the top protein engineering and structure prediction signals from Dec 28 - Jan 04, 2026.

Issue #13: AlphaFold for Docking Screens.

Protein Design Digest - 2026-01-04 - AlphaFold for Docking Screens.

Issue #12: AlphaFold for Docking Screens.

Protein Design Digest - 2026-01-04 - AlphaFold for Docking Screens.

Issue #12: Integrated cytotoxicity screening and in silico analysis of coumarin nucleoside conjugates as computationally modeled VEGFR-2 inhibitors: oncocyte cytotoxicity, molecular docking, and dynamics simulation studies.

Protein Design Digest - 2026-01-03 - Integrated cytotoxicity screening and in silico analysis of coumarin nucleoside conjugates as computationally modeled VEGFR-2 inhibitors: oncocyte cytotoxicity, molecular docking, and dynamics simulation studies.

Issue #11: Integrated cytotoxicity screening and in silico analysis of coumarin nucleoside conjugates as computationally modeled VEGFR-2 inhibitors: oncocyte cytotoxicity, molecular docking, and dynamics simulation studies.

Issue #1: Integrated cytotoxicity screening and in silico analysis of coumarin nucleoside conjugates as computationally modeled VEGFR-2 inhibitors: oncocyte cytotoxicity, molecular docking, and dynamics simulation studies.

Issue #1: Integrated cytotoxicity screening and in silico analysis of coumarin nucleoside conjugates as computationally modeled VEGFR-2 inhibitors: oncocyte cytotoxicity, molecular docking, and dynamics simulation studies.

Protein Design Digest - 2026-01-02 - Integrated cytotoxicity screening and in silico analysis of coumarin nucleoside conjugates as computationally modeled VEGFR-2 inhibitors: oncocyte cytotoxicity, molecular docking, and dynamics simulation studies.

Issue #10: Integrated cytotoxicity screening and in silico analysis of coumarin nucleoside conjugates as computationally modeled VEGFR-2 inhibitors: oncocyte cytotoxicity, molecular docking, and dynamics simulation studies.

Protein Design Digest - 2026-01-01 - Integrated cytotoxicity screening and in silico analysis of coumarin nucleoside conjugates as computationally modeled VEGFR-2 inhibitors: oncocyte cytotoxicity, molecular docking, and dynamics simulation studies.

Issue #1: Integrated cytotoxicity screening and in silico analysis of coumarin nucleoside conjugates as computationally modeled VEGFR-2 inhibitors: oncocyte cytotoxicity, molecular docking, and dynamics simulation studies.

Issue #9: Integrated cytotoxicity screening and in silico analysis of coumarin nucleoside conjugates as computationally modeled VEGFR-2 inhibitors: oncocyte cytotoxicity, molecular docking, and dynamics simulation studies.

Protein Design Digest - 2025-12-31 - Integrated cytotoxicity screening and in silico analysis of coumarin nucleoside conjugates as computationally modeled VEGFR-2 inhibitors: oncocyte cytotoxicity, molecular docking, and dynamics simulation studies.

Issue #1: Integrated cytotoxicity screening and in silico analysis of coumarin nucleoside conjugates as computationally modeled VEGFR-2 inhibitors: oncocyte cytotoxicity, molecular docking, and dynamics simulation studies.

Issue #8: Integrated cytotoxicity screening and in silico analysis of coumarin nucleoside conjugates as computationally modeled VEGFR-2 inhibitors: oncocyte cytotoxicity, molecular docking, and dynamics simulation studies.

Protein Design Digest - 2025-12-30 - Integrated cytotoxicity screening and in silico analysis of coumarin nucleoside conjugates as computationally modeled VEGFR-2 inhibitors: oncocyte cytotoxicity, molecular docking, and dynamics simulation studies.

Issue #1: Integrated cytotoxicity screening and in silico analysis of coumarin nucleoside conjugates as computationally modeled VEGFR-2 inhibitors: oncocyte cytotoxicity, molecular docking, and dynamics simulation studies.

Issue #7: Integrated cytotoxicity screening and in silico analysis of coumarin nucleoside conjugates as computationally modeled VEGFR-2 inhibitors: oncocyte cytotoxicity, molecular docking, and dynamics simulation studies.

Protein Design Digest - 2025-12-29 - Integrated cytotoxicity screening and in silico analysis of coumarin nucleoside conjugates as computationally modeled VEGFR-2 inhibitors: oncocyte cytotoxicity, molecular docking, and dynamics simulation studies.

Issue #1: Integrated cytotoxicity screening and in silico analysis of coumarin nucleoside conjugates as computationally modeled VEGFR-2 inhibitors: oncocyte cytotoxicity, molecular docking, and dynamics simulation studies.

Weekly Digest: Dec 21 - Dec 28, 2025

A curated summary of the top protein engineering and structure prediction signals from Dec 21 - Dec 28, 2025.

Issue #7: Integrated cytotoxicity screening and in silico analysis of coumarin nucleoside conjugates as computationally modeled VEGFR-2 inhibitors: oncocyte cytotoxicity, molecular docking, and dynamics simulation studies.

Protein Design Digest - 2025-12-28 - Integrated cytotoxicity screening and in silico analysis of coumarin nucleoside conjugates as computationally modeled VEGFR-2 inhibitors: oncocyte cytotoxicity, molecular docking, and dynamics simulation studies.

Issue #5: Integrated cytotoxicity screening and in silico analysis of coumarin nucleoside conjugates as computationally modeled VEGFR-2 inhibitors: oncocyte cytotoxicity, molecular docking, and dynamics simulation studies.

Protein Design Digest - 2025-12-27 - Integrated cytotoxicity screening and in silico analysis of coumarin nucleoside conjugates as computationally modeled VEGFR-2 inhibitors: oncocyte cytotoxicity, molecular docking, and dynamics simulation studies.

Issue #1: Integrated cytotoxicity screening and in silico analysis of coumarin nucleoside conjugates as computationally modeled VEGFR-2 inhibitors: oncocyte cytotoxicity, molecular docking, and dynamics simulation studies.

Issue #1: Integrated cytotoxicity screening and in silico analysis of coumarin nucleoside conjugates as computationally modeled VEGFR-2 inhibitors: oncocyte cytotoxicity, molecular docking, and dynamics simulation studies.

Protein Design Digest - 2025-12-26 - Integrated cytotoxicity screening and in silico analysis of coumarin nucleoside conjugates as computationally modeled VEGFR-2 inhibitors: oncocyte cytotoxicity, molecular docking, and dynamics simulation studies.

Issue #1: Integrated cytotoxicity screening and in silico analysis of coumarin nucleoside conjugates as computationally modeled VEGFR-2 inhibitors: oncocyte cytotoxicity, molecular docking, and dynamics simulation studies.

Protein Design Digest - 2025-12-25 - Integrated cytotoxicity screening and in silico analysis of coumarin nucleoside conjugates as computationally modeled VEGFR-2 inhibitors: oncocyte cytotoxicity, molecular docking, and dynamics simulation studies.

Issue #4: 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.

Protein Design Digest - 2025-12-24 - 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.

Issue #1: 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.

Issue #3: A Comparative Study of Deep Learning and Classical Modeling Approaches for Protein-Ligand Binding Pose and Affinity Prediction in Coronavirus Main Proteases.

Protein Design Digest - 2025-12-23 - A Comparative Study of Deep Learning and Classical Modeling Approaches for Protein-Ligand Binding Pose and Affinity Prediction in Coronavirus Main Proteases.

Issue #1: 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.

Protein Design Digest - 2025-12-23 - 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.

Issue #3: 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.

Protein Design Digest - 2025-12-22 - 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.

Issue #2: 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.

Weekly Digest: Dec 14 - Dec 21, 2025

A curated summary of the top protein engineering and structure prediction signals from Dec 14 - Dec 21, 2025.

Issue #2: Meeko: Molecule Parametrization and Software Interoperability for Docking and Beyond.

Protein Design Digest - 2025-12-21 - Meeko: Molecule Parametrization and Software Interoperability for Docking and Beyond.

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