From Code to Fold

Reading List

Reading List

Essential textbooks, research papers, and supplementary materials for mastering protein design

Required Textbooks

Molecular Biology of the Cell

Alberts et al. • 6th Edition (2014)

Garland Science

ISBN: 978-0815344322

Comprehensive foundation in cell biology with excellent protein structure coverage.

Relevant Chapters:

  • Chapter 3: Proteins
  • Chapter 4: DNA, Chromosomes and Genomes
Access Online
Introduction to Protein Structure

Branden & Tooze • 2nd Edition (1999)

Garland Science

ISBN: 978-0815323051

Classic text focusing specifically on protein structure and folding principles.

Relevant Chapters:

  • All chapters recommended
Access Online
Bioinformatics and Functional Genomics

Pevsner, J. • 3rd Edition (2015)

Wiley-Blackwell

ISBN: 978-1118581780

Modern computational approaches to protein analysis and structure prediction.

Relevant Chapters:

  • Chapter 11: Protein Analysis
  • Chapter 12: Protein Structure
Access Online

Complete Weekly Reading Schedule

Comprehensive reading assignments for all 14 weeks of the interdisciplinary protein design curriculum, covering foundational biology through advanced AI applications.

Week 1
Proteins as Biological Machines

Molecular Biology of the Cell, Ch. 4: Proteins

Alberts et al. • NCBI Books (2014)

Introduction to Protein Structure (NCBI primer)

NCBI • Primer (2011)

View Week 1
Week 2
Mathematical Foundations: Geometry & Symmetry

Symmetry in Chemistry

Lachance • LibreTexts (2023)

IUCr Symmetry resources

International Union of Crystallography • Educational Resource (2020)

View Week 2
Week 3
Levels of Protein Structure

Protein Structure

Nature Education • Nature Scitable (2014)

Guide to Understanding PDB Data: Primary Structure

RCSB PDB • Tutorial (2023)

View Week 3
Week 4
Forces Shaping Proteins

Dominant forces in protein folding

Dill, K.A. • Biochemistry (1990)

Protein Structure Overview

Khan Academy • Educational Resource (2023)

View Week 4
Week 5
Biosynthesis in Nature & Synthetic Biology

Translation: DNA to mRNA to Protein

Nature Education • Nature Scitable (2014)

Cell-free protein synthesis review

Various • ACS Synthetic Biology (2019)

View Week 5
Week 6
Protein Geometry & Topology

Protein knots and fold complexity

Taylor, W.R. • Nature (2000)

Protein contact maps tutorial

Various • BMC Bioinformatics (2018)

View Week 6
Week 7
Protein Modeling Basics

SwissModel Tutorial

Swiss Institute of Bioinformatics • Tutorial (2023)

Intro to Comparative Modeling

Various • Nature Protocols (2006)

View Week 7
Week 8
Molecular Dynamics & Simulation

OpenMM Documentation

OpenMM Team • Documentation (2023)

MD Simulations overview

Various • Nature Methods (2013)

View Week 8
Week 9
Thermodynamics & Energy Landscapes

The Protein-Folding Problem, 50 Years On

Dill & MacCallum • Science (2012)

Protein folding landscape review

Various • Annual Review of Biophysics (2013)

View Week 9
Week 10
AI & Machine Learning in Protein Design

Highly accurate protein structure prediction with AlphaFold

Jumper et al. • Nature (2021)

ML in protein engineering review

Various • Nature Reviews Molecular Cell Biology (2022)

View Week 10
Week 11
Enzyme Design & Catalysis

Frances Arnold Nobel Lecture

Arnold, F.H. • Nobel Lecture (2018)

Enzyme Design Review

Various • Nature Chemical Biology (2016)

View Week 11
Week 12
Proteins in Medicine & Materials

Antibodies as drugs

Various • Science (2017)

Proteins in nanomaterials

Various • Nature Materials (2007)

View Week 12
Week 13
Case Studies in Protein Design

De novo protein design review

Various • Annual Review of Biochemistry (2000)

Foldit citizen science

Foldit Team • Interactive Platform (2023)

View Week 13
Week 14
Capstone Project & Presentations

Rosetta Commons Tutorials

Rosetta Commons • Tutorial Collection (2023)

Student-selected papers

Various • Project-specific (2024)

View Week 14

Supplementary Materials

Review Articles
  • Protein folding and misfolding diseases (Dobson, 2003)
  • Computational protein design (Kuhlman & Bradley, 2019)
  • Machine learning in structural biology (AlQuraishi, 2019)
  • Cryo-EM revolution in structural biology (Cheng, 2015)
Historical Papers
  • Protein denaturation (Anfinsen, 1973)
  • Levinthal paradox (Levinthal, 1969)
  • Ramachandran plot (Ramachandran et al., 1963)
  • Secondary structure prediction (Chou & Fasman, 1974)
Recent Advances
  • AlphaFold protein structure prediction (Jumper et al., 2021)
  • De novo protein design (Huang et al., 2022)
  • Protein language models (Rives et al., 2021)
  • Cryo-EM at atomic resolution (Nakane et al., 2020)