Normal Mode Analysis (NMA) and Elastic Network Model (ENM)

• Konrad Hinsen, Normal mode theory and harmonic potential approximations
• A.R. Atilgan et al., Anisotropy of fluctuation dynamics of proteins with an elastic network model, Biophys. J. 2001.
• T. Lin, G. Song, Generalized spring tensor models for protein fluctuation dynamics and conformation changes, BMC Struct Biol. 2010
• M. M. Tirion, Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis, Phys. Rev. Lett. 1905.
• J. Schlitter, Estimation of absolute and relative entropies of macromolecules using the covariance matrix, Chem. Phys. Lett. 1993. - Calculating vibrational entropy
• H. Lee Woodcock, et al., "Vibrational subsystem analysis: A method for probing free energies and correlations in the harmonic limit," J Chem Phys. 129, 214109 (2008). doi: 10.1063/1.3013558
• An Ghysels, et al., "Comparative study of various normal mode analysis techniques based on partial Hessians", J Comput Chem. 2010. doi: 10.1002/jcc.21386

Topological Data Analysis (TDA)

• YouTube: Signature Features in Topological Data Analysis
• Topological Data Analysis with Mapper Algorithm

Rapidly-exploring Random Tree (RRT)

• Wikipedia: Rapidly-exploring random tree

Drug Design

• AI for Drug Design - Lecture 16 - Deep Learning in the Life Sciences (MIT Deep Learning in Life Sciences - Spring 2021)
• B. Sanchez-Lengeling, A. Aspuru-Guzik, Inverse molecular design using machine learning: Generative models for matter engineering, Science, 2018
• A. Nigam, R. Pollice, A. Aspuru-Guzik*, Parallel tempered genetic algorithm guided by deep neural networks for inverse molecular design, Digital Discovery, 2022

Computational Biology Courses/Lectures

• Online Course - Introduction to proteins: structure, function, and motion
• YouTube: [강연] 세포는 외부 신호를 어떻게 감지할까? _최희정 ㅣ 2021 가을 카오스강연 〈과학의 희열〉 4강