Referenced Papers (13)
The RCSB PDB "Molecule of the Month": Inspiring a molecular view of biology
David S Goodsell, Shuchismita Dutta, Christine Zardecki, Maria Voigt, Helen M Berman, Stephen K Burley
PLoS Biol., 2015
"The speaker uses an image from this paper to illustrate the wide variety of protein and protein complex structures that carry out all essential biological processes."
Steered molecular dynamics simulations reveal critical residues for (un)binding of substrates, inhibitors and a product to the malarial M1 aminopeptidase
Daniel S Moore, Conor Brines, Heather Jewhurst, John P Dalton, Irina G Tikhonova
PLoS Comput. Biol., 2018
"This paper is cited to provide an example (M1 Aminopeptidase) of how local fluctuations in protein structure, specifically within binding pockets, are critical for function."
AI-based structure prediction empowers integrative structural analysis of human nuclear pores
Shyamal Mosalaganti, Agnieszka Obarska-Kosinska, Marc Siggel, Reiya Taniguchi, Beata Turoňová, Christian E Zimmerli
Science, 2022
"This paper's work on the Nuclear Pore Complex is used as an example of a large-scale protein complex where hundreds of subunits interact to perform a function, highlighting the importance of dynamic structure across multiple scales."
Cryo-EM structure of the Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine
Wilson Wong, Xiao-Chen Bai, Alan Brown, Israel S Fernandez, Eric Hanssen, Melanie Condron
Elife, 2014
"This paper is listed as an example of research using Cryo-EM, one of the experimental techniques for determining protein structure."
Spatially resolved spectroscopy of the globular cluster RZ 2109 and the nature of its black hole
Mark B Peacock, Stephen E Zepf, Arunav Kundu, Thomas J Maccarone, Katherine L Rhode, John J Salzer
arXiv [astro-ph.GA], 2012
"Cited as an example of a study using Crystallography, an experimental method for protein structure determination."
Highly accurate protein structure prediction with AlphaFold
John Jumper, Richard Evans, Alexander Pritzel, Tim Green, Michael Figurnov, Olaf Ronneberger
Nature, 2021
"This paper, likely the AlphaFold paper, is cited as the prime example of a statistical method for protein structure prediction."
Computational methods for single-particle electron cryomicroscopy
Amit Singer, Fred J Sigworth
Annu. Rev. Biomed. Data Sci., 2020
"This paper is cited as the source for the maximum likelihood objective formulation used in classical cryo-EM reconstruction."
CryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination
PUNJANI
Nat. Methods
"This paper introducing CryoSPARC is cited for its innovation of using gradient descent to find a good starting volume for the EM algorithm, helping to find the global optimum."
RELION: implementation of a Bayesian approach to cryo-EM structure determination
Sjors H W Scheres
J. Struct. Biol., 2012
"This citation for the RELION software package is used to introduce the Bayesian framework (MAP estimation) for reconstruction, which helps prevent overfitting to noise through regularization."
HEALPix: A framework for high-resolution discretization and fast analysis of data distributed on the sphere
K Gorski, E Hivon, A Banday, Benjamin Dan Wandelt, F Hansen, M Reinecke
The Astrophysical Journal, 2004
"The HEALPix framework from this paper is shown as a method for discretizing the pose space, although the speaker concludes a brute-force search using this method is intractable."
CryoDRGN2: Ab initio neural reconstruction of 3D protein structures from real cryo-EM images
Ellen D Zhong, Adam K Lerer, Joey Davis, B Berger
ICCV, 2021
"This paper, introducing CryoDRGN, is cited as an example of a method that uses a hierarchical grid search to efficiently sample pose space, starting coarse and then refining in promising areas."
Structure of human telomerase holoenzyme with bound telomeric DNA
George E Ghanim, Adam J Fountain, Anne-Marie M van Roon, Ramya Rangan, Rhiju Das, Kathleen Collins
Nature, 2021
"An image from this paper illustrates the ad-hoc and iterative nature of traditional 3D classification pipelines, which the speaker notes as a practical challenge."
3DFlex: determining structure and motion of flexible proteins from cryo-EM
Ali Punjani, David J Fleet
Nat. Methods, 2023
"This paper is listed as an example of a "flow field" method, a type of non-linear parameterization for modeling continuous structural heterogeneity."