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1,005 claims from 629 papers are on the record. 39 have been checked so far; the other 966 have no check with a result yet.

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Status: Unchecked ×Topic: Protein Structure and Dynamics ×Clear all

20 claims from 13 papers

1. Biochemistry, Genetics and Molecular Biology › Protein Structure and Dynamics

   AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models

   Váradi, Anyango, Deshpande et al. · Nucleic Acids Research · 2021

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   1. Unchecked“Powered by AlphaFold v2.0 of DeepMind, it has enabled an unprecedented expansion of the structural coverage of the known protein-sequence space.”
   2. Unchecked“The initial release of AlphaFold DB contains over 360,000 predicted structures across 21 model-organism proteomes, which will soon be expanded to cover most of the (over 100 million) representative sequences from the UniRef90 data set.”

2. Biochemistry, Genetics and Molecular Biology › Protein Structure and Dynamics

   Comparison of multiple Amber force fields and development of improved protein backbone parameters

   Horn̆ák, Abel, Okur, Strockbine, Roitberg and Simmerling · Proteins Structure Function and Bioinformatics · 2006

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   1. Unchecked“This parameter set, which we denote ff99SB, achieves a better balance of secondary structure elements as judged by improved distribution of backbone dihedrals for glycine and alanine with respect to PDB survey data.”

3. Biochemistry, Genetics and Molecular Biology › Protein Structure and Dynamics

   Evolutionary-scale prediction of atomic-level protein structure with a language model

   Lin, Akin, Rao et al. · Science · 2023

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   1. Unchecked“We demonstrate direct inference of full atomic-level protein structure from primary sequence using a large language model.”

4. Biochemistry, Genetics and Molecular Biology › Protein Structure and Dynamics

   Protein complex prediction with AlphaFold-Multimer

   Evans, O’Neill, Pritzel et al. · bioRxiv (Cold Spring Harbor Laboratory) · 2021

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   1. Unchecked“On a benchmark dataset of 17 heterodimer proteins without templates (introduced in [2]) we achieve at least medium accuracy (DockQ [3] ≥ 0.49) on 13 targets and high accuracy (DockQ ≥ 0.8) on 7 targets, compared to 9 targets of at least medium accuracy and 4…
   2. Unchecked“For heteromeric interfaces we successfully predict the interface (DockQ ≥ 0.23) in 70% of cases, and produce high accuracy predictions (DockQ ≥ 0.8) in 26% of cases, an improvement of +27 and +14 percentage points over the flexible linker modification of Alp…
   3. Unchecked“For homomeric inter-faces we successfully predict the interface in 72% of cases, and produce high accuracy predictions in 36% of cases, an improvement of +8 and +7 percentage points respectively.”

5. Biochemistry, Genetics and Molecular Biology › Protein Structure and Dynamics

   Improved protein structure prediction using potentials from deep learning

   Senior, Evans, Jumper et al. · Nature · 2020

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   1. Unchecked“We find that the resulting potential can be optimized by a simple gradient descent algorithm to generate structures without complex sampling procedures.”
   2. Unchecked“In the recent Critical Assessment of Protein Structure Prediction 5 (CASP13)-a blind assessment of the state of the field-AlphaFold created high-accuracy structures (with template modelling (TM) scores 6 of 0.7 or higher) for 24 out of 43 free modelling doma…

6. Biochemistry, Genetics and Molecular Biology › Protein Structure and Dynamics

   Highly accurate protein structure prediction for the human proteome

   Tunyasuvunakool, Adler, Wu et al. · Nature · 2021

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   1. Unchecked“The resulting dataset covers 58% of residues with a confident prediction, of which a subset (36% of all residues) have very high confidence.”

7. Biochemistry, Genetics and Molecular Biology › Protein Structure and Dynamics

   Fast and accurate protein structure search with Foldseek

   van Kempen, Kim, Tumescheit et al. · Nature Biotechnology · 2023

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   1. Unchecked“Foldseek decreases computation times by four to five orders of magnitude with 86%, 88% and 133% of the sensitivities of Dali, TM-align and CE, respectively.”

8. Biochemistry, Genetics and Molecular Biology › Protein Structure and Dynamics

   Unified rational protein engineering with sequence-based deep representation learning

   Alley, Khimulya, Biswas, AlQuraishi and Church · Nature Methods · 2019

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   1. Unchecked“We show that the simplest models built on top of this unified representation (UniRep) are broadly applicable and generalize to unseen regions of sequence space.”
   2. Unchecked“Our data-driven approach predicts the stability of natural and de novo designed proteins, and the quantitative function of molecularly diverse mutants, competitively with the state-of-the-art methods.”
   3. Unchecked“UniRep further enables two orders of magnitude efficiency improvement in a protein engineering task.”

9. Biochemistry, Genetics and Molecular Biology › Protein Structure and Dynamics

   lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests

   Mariani, Biasini, Barbato and Schwede · Bioinformatics · 2013

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   1. Unchecked“We demonstrate that lDDT is well suited to assess local model quality, even in the presence of domain movements, while maintaining good correlation with global measures.”

10. Biochemistry, Genetics and Molecular Biology › Protein Structure and Dynamics

    Improved prediction of protein-protein interactions using AlphaFold2

    Bryant, Pozzati and Elofsson · Nature Communications · 2022

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    1. Unchecked“We find that the AlphaFold2 protocol together with optimised multiple sequence alignments, generate models with acceptable quality (DockQ ≥ 0.23) for 63% of the dimers.”
    2. Unchecked“From the predicted interfaces we create a simple function to predict the DockQ score which distinguishes acceptable from incorrect models as well as interacting from non-interacting proteins with state-of-art accuracy.”

11. Biochemistry, Genetics and Molecular Biology › Protein Structure and Dynamics

    Simulating 500 million years of evolution with a language model

    Hayes, Rao, Akin et al. · Science · 2025

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    1. Unchecked“Among the generations that we synthesized, we found a bright fluorescent protein at a far distance (58% sequence identity) from known fluorescent proteins, which we estimate is equivalent to simulating 500 million years of evolution.”

12. Biochemistry, Genetics and Molecular Biology › Protein Structure and Dynamics

    A structural biology community assessment of AlphaFold2 applications

    Akdel, Pires, Porta‐Pardo et al. · Nature Structural & Molecular Biology · 2022

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    1. Unchecked“For 11 proteomes, an average of 25% additional residues can be confidently modeled when compared with homology modeling, identifying structural features rarely seen in the Protein Data Bank.”

13. Biochemistry, Genetics and Molecular Biology › Protein Structure and Dynamics

    Scaffolding protein functional sites using deep learning

    Wang, Lisanza, Juergens et al. · Science · 2022

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    1. Unchecked“The first approach, “constrained hallucination,” optimizes sequences such that their predicted structures contain the desired functional site.”