Integrating model simulation tools and cryo‐electron microscopy
JG Beton, T Cragnolini, M Kaleel… - Wiley …, 2023 - Wiley Online Library
The power of computer simulations, including machine‐learning, has become an
inseparable part of scientific analysis of biological data. This has significantly impacted the …
inseparable part of scientific analysis of biological data. This has significantly impacted the …
Advances in structure modeling methods for cryo-electron microscopy maps
E Alnabati, D Kihara - Molecules, 2019 - mdpi.com
Cryo-electron microscopy (cryo-EM) has now become a widely used technique for structure
determination of macromolecular complexes. For modeling molecular structures from …
determination of macromolecular complexes. For modeling molecular structures from …
Multiple subunit fitting into a low-resolution density map of a macromolecular complex using a gaussian mixture model
T Kawabata - Biophysical journal, 2008 - cell.com
Recently, electron microscopy measurement of single particles has enabled us to
reconstruct a low-resolution 3D density map of large biomolecular complexes. If structures of …
reconstruct a low-resolution 3D density map of large biomolecular complexes. If structures of …
Inferential optimization for simultaneous fitting of multiple components into a CryoEM map of their assembly
Models of macromolecular assemblies are essential for a mechanistic description of cellular
processes. Such models are increasingly obtained by fitting atomic-resolution structures of …
processes. Such models are increasingly obtained by fitting atomic-resolution structures of …
A machine learning approach for the identification of protein secondary structure elements from electron cryo‐microscopy density maps
The accuracy of the secondary structure element (SSE) identification from volumetric protein
density maps is critical for de‐novo backbone structure derivation in electron cryo …
density maps is critical for de‐novo backbone structure derivation in electron cryo …
ADP_EM: fast exhaustive multi-resolution docking for high-throughput coverage
Motivation: Efficient fitting tools are needed to take advantage of a fast growth of atomic
models of protein domains from crystallography or comparative modeling, and low …
models of protein domains from crystallography or comparative modeling, and low …
Using Sculptor and Situs for simultaneous assembly of atomic components into low-resolution shapes
S Birmanns, M Rusu, W Wriggers - Journal of structural biology, 2011 - Elsevier
We describe an integrated software system called Sculptor that combines visualization
capabilities with molecular modeling algorithms for the analysis of multi-scale data sets …
capabilities with molecular modeling algorithms for the analysis of multi-scale data sets …
Determining macromolecular assembly structures by molecular docking and fitting into an electron density map
Structural models of macromolecular assemblies are instrumental for gaining a mechanistic
understanding of cellular processes. Determining these structures is a major challenge for …
understanding of cellular processes. Determining these structures is a major challenge for …
Artificial intelligence advances for de novo molecular structure modeling in cryo‐electron microscopy
Cryo‐electron microscopy (cryo‐EM) has become a major experimental technique to
determine the structures of large protein complexes and molecular assemblies, as …
determine the structures of large protein complexes and molecular assemblies, as …
Beta-sheet detection and representation from medium resolution cryo-EM density maps
Secondary structure element (SSE) identification from volumetric protein density maps is
critical for de-novo backbone structure derivation in electron cryo-microscopy (cryoEM) …
critical for de-novo backbone structure derivation in electron cryo-microscopy (cryoEM) …