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Protein assembly by design
J Zhu, N Avakyan, A Kakkis, AM Hoffnagle… - Chemical …, 2021 - ACS Publications
Proteins are nature's primary building blocks for the construction of sophisticated molecular
machines and dynamic materials, ranging from protein complexes such as photosystem II …
machines and dynamic materials, ranging from protein complexes such as photosystem II …
Advances in protein structure prediction and design
The prediction of protein three-dimensional structure from amino acid sequence has been a
grand challenge problem in computational biophysics for decades, owing to its intrinsic …
grand challenge problem in computational biophysics for decades, owing to its intrinsic …
Abdiffuser: full-atom generation of in-vitro functioning antibodies
K Martinkus, J Ludwiczak, WC Liang… - Advances in …, 2023 - proceedings.neurips.cc
We introduce AbDiffuser, an equivariant and physics-informed diffusion model for the joint
generation of antibody 3D structures and sequences. AbDiffuser is built on top of a new …
generation of antibody 3D structures and sequences. AbDiffuser is built on top of a new …
EMRinger: side chain–directed model and map validation for 3D cryo-electron microscopy
Advances in high-resolution cryo-electron microscopy (cryo-EM) require the development of
validation metrics to independently assess map quality and model geometry. We report …
validation metrics to independently assess map quality and model geometry. We report …
An end-to-end deep learning method for protein side-chain packing and inverse folding
M McPartlon, J Xu - Proceedings of the National Academy of Sciences, 2023 - pnas.org
Protein side-chain packing (PSCP), the task of determining amino acid side-chain
conformations given only backbone atom positions, has important applications to protein …
conformations given only backbone atom positions, has important applications to protein …
GalaxyRefine: Protein structure refinement driven by side-chain repacking
The quality of model structures generated by contemporary protein structure prediction
methods strongly depends on the degree of similarity between the target and available …
methods strongly depends on the degree of similarity between the target and available …
A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions
MV Shapovalov, RL Dunbrack - Structure, 2011 - cell.com
Rotamer libraries are used in protein structure determination, prediction, and design. The
backbone-dependent rotamer library consists of rotamer frequencies, mean dihedral angles …
backbone-dependent rotamer library consists of rotamer frequencies, mean dihedral angles …
UCSF Chimera, MODELLER, and IMP: an integrated modeling system
Z Yang, K Lasker, D Schneidman-Duhovny… - Journal of structural …, 2012 - Elsevier
Structural modeling of macromolecular complexes greatly benefits from interactive
visualization capabilities. Here we present the integration of several modeling tools into …
visualization capabilities. Here we present the integration of several modeling tools into …
Protein structure prediction: conventional and deep learning perspectives
VA Jisna, PB Jayaraj - The protein journal, 2021 - Springer
Protein structure prediction is a way to bridge the sequence-structure gap, one of the main
challenges in computational biology and chemistry. Predicting any protein's accurate …
challenges in computational biology and chemistry. Predicting any protein's accurate …
Improved prediction of protein side‐chain conformations with SCWRL4
GG Krivov, MV Shapovalov… - … Structure, Function, and …, 2009 - Wiley Online Library
Determination of side-chain conformations is an important step in protein structure prediction
and protein design. Many such methods have been presented, although only a small …
and protein design. Many such methods have been presented, although only a small …