"Comparing protein structures with Clojure" by Blaine Mooers

Protein Structure and Comparison

• Comparing protein structures involves aligning amino acid sequences and superimposing structures.
• Protein structure determines function, and small changes in sequence can result in significant changes in function.
• X-ray crystallography is a common method for determining protein structure, but has limitations, such as challenging to create large crystals.
• NMR (Nuclear Magnetic Resonance) is another method, but has lower accuracy than X-ray crystallography.
• Probabilistic programming approaches can be used for structure comparison, such as THESEUS MAP.
• THESEUS MAP uses Hamiltonian Monte Carlo (HMC) to reduce noise in data and improve structure alignment.
• HMC is more efficient than random walk sampling approaches.
• C alpha carbon atoms are important for understanding protein structure and can be used to visualize alpha helices and beta strands.
• Protein structure prediction tools like AlphaFold can be used to compare predicted and experimental structures.
• Comparing predicted and experimental structures can help understand why certain changes in protein sequence result in changes in function.
• Protecting proteins from aggregation is important for function, and small changes in sequence can affect aggregation properties.
• Mutations can occur in proteins, leading to changes in function, and understanding these changes is important for disease diagnosis and treatment.
• Researchers have developed models to predict protein structure and compare experimental and predicted structures, such as THESEUS and THESEUS PP.
• THESEUS and THESEUS PP use probabilistic programming approaches to reduce noise in data and improve structure alignment.
• Portsmouth and colleagues have developed a version of THESEUS called THESEUS-HMC that uses HMC to reduce noise in data and improve structure alignment.
• Modeling protein structure and function is important for understanding biological systems and developing new treatments for diseases.
• Comparing predicted and experimental structures can help understand why certain changes in protein sequence result in changes in function.