ArticleProteins2012
Rotamer libraries and probabilities of transition between rotamers for the side chains in protein-protein binding.
Article in Proteins, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
19 citing papers in PubMed.
- Crystal structures reveal phosphorylation-dependent disruption of the heat shock protein 70-CHIP interface: A compensatory G132N variant restores binding affinity.Cell stress & chaperones · 2026Article
- Parsing Dynamics of Protein Backbone NH and Side-Chain Methyl Groups using Molecular Dynamics Simulations.Journal of chemical theory and computation · 2024Article
- Dockground resource for protein recognition studies.Protein science : a publication of the Protein Society · 2022Article
- Exploiting Sequence-Dependent Rotamer Information in Global Optimization of Proteins.The journal of physical chemistry. B · 2022Article
- Docking-based long timescale simulation of cell-size protein systems at atomic resolution.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Computational reconstruction of atomistic protein structures from coarse-grained models.Computational and structural biotechnology journal · 2020Review
- ccPDB 2.0: an updated version of datasets created and compiled from Protein Data Bank.Database : the journal of biological databases and curation · 2019Article
- Computational Feasibility of an Exhaustive Search of Side-Chain Conformations in Protein-Protein Docking.Journal of computational chemistry · 2018Article
- Dockground: A comprehensive data resource for modeling of protein complexes.Protein science : a publication of the Protein Society · 2018Article
- Side-Chain Conformational Preferences Govern Protein-Protein Interactions.Journal of the American Chemical Society · 2016Article
- Article
- A three dimensional visualisation approach to protein heavy-atom structure reconstruction.BMC structural biology · 2014Article
- Protein-protein docking: from interaction to interactome.Biophysical journal · 2014Review
- Assessment of protein side-chain conformation prediction methods in different residue environments.Proteins · 2014Article
- Ensemble-based characterization of unbound and bound states on protein energy landscape.Protein science : a publication of the Protein Society · 2013Article
- Low-resolution structural modeling of protein interactome.Current opinion in structural biology · 2013Review
- A comparison of successful and failed protein interface designs highlights the challenges of designing buried hydrogen bonds.Protein science : a publication of the Protein Society · 2013Article
- Correlation analysis of the side-chains conformational distribution in bound and unbound proteins.BMC bioinformatics · 2012Article
- The multifaceted helical net of amphipathic alpha-helices; the next dimension of the helical peptide wheel.Science progressArticle
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
Conformational changes in the side chains are essential for protein-protein binding. Rotameric states and unbound- to-bound conformational changes in the surface residues were systematically studied on a representative set of protein complexes. The side-chain conformations were mapped onto dihedral angles space. The variable threshold algorithm was developed to cluster the dihedral angle distributions and to derive rotamers, defined as the most probable conformation in a cluster. Six rotamer libraries were generated: full surface, surface noninterface, and surface interface-each for bound and unbound states. The libraries were used to calculate the probabilities of the rotamer transitions upon binding. The stability of amino acids was quantified based on the transition maps. The noninterface residues' stability was higher than that of the interface. Long side chains with three or four dihedral angles were less stable than the shorter ones. The transitions between the rotamers at the interface occurred more frequently than on the noninterface surface. Most side chains changed conformation within the same rotamer or moved to an adjacent rotamer. The highest percentage of the transitions was observed primarily between the two most occupied rotamers. The probability of the transition between rotamers increased with the decrease of the rotamer stability. The analysis revealed characteristics of the surface side-chain conformational transitions that can be utilized in flexible docking protocols.
Indexed as
Identifiers
What OpenQuestion holds
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.