ReviewCurrent opinion in structural biology2021
The role of local versus nonlocal physicochemical restraints in determining protein native structure.
Review in Current opinion in structural biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
9 citing papers in PubMed.
- Article
- Exploring binding positions and backbone conformations of peptide ligands of proteins with a backbone-centred statistical energy function.Journal of computer-aided molecular design · 2023Article
- Mechanism of ultrasonic combined with different fields on protein complex system and its effect on its functional characteristics and application: A review.Ultrasonics sonochemistry · 2023Review
- Local Backbone Geometry Plays a Critical Role in Determining Conformational Preferences of Amino Acid Residues in Proteins.Biomolecules · 2022Article
- Article
- rsRNASP: A residue-separation-based statistical potential for RNA 3D structure evaluation.Biophysical journal · 2022Article
- High-Performance Deep Learning Toolbox for Genome-Scale Prediction of Protein Structure and Function.Workshop on Machine Learning in HPC Environments. Workshop on Machine Learning in HPC Environments · 2021Article
- AlphaFold 2: Why It Works and Its Implications for Understanding the Relationships of Protein Sequence, Structure, and Function.Journal of chemical information and modeling · 2021Article
- On the emergence of homochirality and life itself.The biochemist · 2021Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
The tertiary structure of a native protein is dictated by the interplay of local secondary structure propensities, hydrogen bonding, and tertiary interactions. It is argued that the space of known protein topologies covers all single domain folds and results from the compactness of the native structure and excluded volume. Protein compactness combined with the chirality of the protein's side chains also yields native-like Ramachandran plots. It is the many-body, tertiary interactions among residues that collectively select for the global structure that a particular protein sequence adopts. This explains why the recent advances in deep-learning approaches that predict protein side-chain contacts, the distance matrix between residues, and sequence alignments are successful. They succeed because they implicitly learned the many-body interactions among protein residues.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.