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Hand-picked guides to accelerate your learning

Understanding pLDDT Confidence Scores
Featured Article
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.

P

Protogen Team

Computational Biologists

MSA Quality & Why It Matters for Structure Prediction
Featured Article
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.

P

Protogen Team

Computational Biologists

Recent Articles

Latest guides and tutorials

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
P

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.

alphafoldanalysistutorial
P

Protogen Team

Computational Biologists

Read
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
P

Protogen Team

Computational Biologists

Read
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.

alphafoldesmfoldresearch
P

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.

biochemistrytutorialalphafold
P

Protogen Team

Educators

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Curated Learning Paths

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Getting Started

Perfect for newcomers to protein structure prediction

5 articlesStart Learning →

Advanced Analysis

Deep dive into result interpretation and validation

8 articlesStart Learning →

Research & Applications

Real-world case studies and research workflows

6 articlesStart Learning →

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