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19 comprehensive guides and tutorials

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High-Throughput Structure Prediction Pipelines
case-study24 min read

High-Throughput Structure Prediction Pipelines

Scale AlphaFold2 for proteome-wide analysis: batch processing, quality control, and resource optimization for thousands of proteins.

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Protogen Team

Infrastructure

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Academic Research Workflow: From Hypothesis to Publication
case-study22 min read

Academic Research Workflow: From Hypothesis to Publication

Complete guide for academic researchers: experimental design, structural analysis, figure preparation, and manuscript writing.

researchresearchresearch
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Protogen Team

Research Support

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Protein-Ligand Docking with AlphaFold2 Structures
case-study20 min read

Protein-Ligand Docking with AlphaFold2 Structures

Integrate structure prediction with virtual screening: prepare structures, define binding sites, and discover hit compounds.

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Protogen Team

Drug Discovery

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Membrane Protein Structure Prediction: GPCRs, Ion Channels, and Transporters
case-study18 min read

Membrane Protein Structure Prediction: GPCRs, Ion Channels, and Transporters

Master the challenges of predicting transmembrane proteins: topology validation, lipid bilayer context, and conformational states.

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Protogen Team

Membrane Protein Specialists

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Antibody-Antigen Structure Prediction for Therapeutic Development
Featured
case-study28 min read

Antibody-Antigen Structure Prediction for Therapeutic Development

Complete workflow for predicting antibody-antigen complexes: from CDR annotation to epitope mapping and affinity maturation guidance.

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Protogen Team

Therapeutic Development

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Predicting Intrinsically Disordered Regions
advanced22 min read

Predicting Intrinsically Disordered Regions

Understand how AlphaFold2 handles protein disorder: learn to distinguish true disorder from prediction failures and interpret low confidence scores correctly.

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Protogen Team

Structural Biologists

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Structural Superposition and RMSD Analysis
intermediate20 min read

Structural Superposition and RMSD Analysis

Master structural comparison techniques: learn to superimpose structures, calculate RMSD, and validate AlphaFold2 predictions against experimental data.

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Protogen Team

Structural Biologists

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Understanding ipTM and pTM Confidence Metrics
Featured
advanced26 min read

Understanding ipTM and pTM Confidence Metrics

Comprehensive guide to interpreting AlphaFold2 confidence scores: learn what pTM and ipTM really measure and how to combine metrics for reliable assessment.

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Protogen Team

Computational Biologists

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Template Selection and Custom MSA Generation
advanced24 min read

Template Selection and Custom MSA Generation

Advanced guide to structural templates and MSA customization: learn when templates help or hurt, and how to optimize MSA searches for difficult targets.

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Protogen Team

Computational Biologists

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Multimer Prediction and Protein Complexes
Featured
intermediate22 min read

Multimer Prediction and Protein Complexes

Master AlphaFold2-Multimer: learn to predict protein complexes, interpret ipTM and interface PAE, and validate predicted interfaces with confidence.

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Protogen Team

Structural Biologists

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Common Mistakes Beginners Make with AlphaFold2
beginner16 min read

Common Mistakes Beginners Make with AlphaFold2

Avoid the most frequent pitfalls when starting with protein structure prediction. Learn what to watch for and how to ensure reliable results.

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Protogen Team

Computational Biologists

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Your First AlphaFold2 Prediction: A Complete Guide
beginner18 min read

Your First AlphaFold2 Prediction: A Complete Guide

Step-by-step walkthrough for running your first protein structure prediction with AlphaFold2, from sequence preparation to results analysis.

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Protogen Team

Computational Biologists

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Drug Discovery with AlphaFold2: A Complete Workflow
Featured
case-study35 min read

Drug Discovery with AlphaFold2: A Complete Workflow

From target identification to lead optimization: learn how predicted structures accelerate drug discovery timelines and reduce costs in real-world case studies.

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Protogen Team

Computational Drug Discovery

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Validation Checklist for Predicted Structures
Featured
advanced30 min read

Validation Checklist for Predicted Structures

A comprehensive quality assurance guide: from confidence metrics to experimental validation, ensuring your AlphaFold2 predictions are publication-ready.

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Protogen Team

Structural Biologists

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Reading and Interpreting PAE Matrices
intermediate20 min read

Reading and Interpreting PAE Matrices

Master the art of reading Predicted Aligned Error matrices to understand domain organization, interface confidence, and relative positioning.

alphafoldanalysistutorial
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Protogen Team

Structural Biologists

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MSA Quality & Why It Matters for Structure Prediction
Featured
intermediate22 min read

MSA Quality & Why It Matters for Structure Prediction

Deep dive into multiple sequence alignments: how they work, why they're crucial for AlphaFold2, and what to do when they fail.

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Protogen Team

Computational Biologists

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Understanding pLDDT Confidence Scores
Featured
beginner8 min read

Understanding pLDDT Confidence Scores

Learn how to interpret per-residue confidence scores from AlphaFold2 predictions and what they mean for your structural analysis.

alphafoldanalysistutorial
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Protogen Team

Computational Biologists

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AlphaFold2 vs ESMFold: When to Use Each
intermediate12 min read

AlphaFold2 vs ESMFold: When to Use Each

Compare the two leading protein structure prediction models and learn which one is best for your research needs.

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Protogen Team

ML Researchers

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Protein Folding: From Sequence to Structure
beginner25 min read

Protein Folding: From Sequence to Structure

A comprehensive guide to the fundamental principles of protein folding, from amino acids to AI-powered prediction.

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Protogen Team

Educators

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