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A critical assessment of the secondary structure α-helices and their termini in proteins

https://doi.org/10.1093/protein/15.7.545
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Outgoing claims: the papers this work cites, builds on, or argues with.

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CASP2: Report on ab initio predictions
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Dissecting α-helices: Position-specific analysis of α-helices in globular proteins
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Evaluation and improvement of multiple sequence methods for protein secondary structure prediction
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New methods for accurate prediction of protein secondary structure
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Application of multiple sequence alignment profiles to improve protein secondary structure prediction
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Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features
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Selection of representative protein data sets
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Comparison of conformational characteristics in structurally similar protein pairs
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N‐ and C‐capping preferences for all 20 amino acids in α‐helical peptides
inferredcites →https://doi.org/10.1002/pro.5560051116openalex-snapshot
Identification and application of the concepts important for accurate and reliable protein secondary structure prediction
inferredcites →https://doi.org/10.1002/pro.5560060117openalex-snapshot
Structures of N‐termini of helices in proteins
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Helix capping
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Searching protein structure databases has come of age
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Knowledge‐based protein secondary structure assignment
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Prediction of Protein Secondary Structure at Better than 70% Accuracy
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Protein Secondary Structure Prediction Using Nearest-neighbor Methods
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The Limits of Protein Secondary Structure Prediction Accuracy from Multiple Sequence Alignment
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Prediction of Protein Secondary Structure by Combining Nearest-neighbor Algorithms and Multiple Sequence Alignments
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Hidden Markov Models in Computational Biology
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Protein Fold Recognition by Mapping Predicted Secondary Structures
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Protein secondary structure prediction using local alignments
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Protein fold recognition by prediction-based threading
inferredcites →https://doi.org/10.1006/jmbi.1998.1682openalex-snapshot
Position dependence of non-polar amino acid intrinsic helical propensities
inferredcites →https://doi.org/10.1006/jmbi.1998.2549openalex-snapshot
Side-chain structures in the first turn of the α-helix 1 1Edited by J. M. Thornton
inferredcites →https://doi.org/10.1006/jmbi.1999.3091openalex-snapshot
Protein secondary structure prediction based on position-specific scoring matrices 1 1Edited by G. Von Heijne
inferredcites →https://doi.org/10.1006/jmbi.1999.3206openalex-snapshot
Periodicity in α-helix lengths and C-capping preferences 1 1Edited by J. M. Thornton
inferredcites →https://doi.org/10.1006/jmbi.2001.4762openalex-snapshot
FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties11Edited by B. Honig
inferredcites →https://doi.org/10.1007/978-1-4612-6137-7openalex-snapshot
Principles of Protein Structure
inferredcites →https://doi.org/10.1016/0022-2836(78)90297-8openalex-snapshot
Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins
inferredcites →https://doi.org/10.1016/0022-2836(87)90292-0openalex-snapshot
Further developments of protein secondary structure prediction using information theory
inferredcites →https://doi.org/10.1016/0022-2836(87)90501-8openalex-snapshot
Prediction of protein secondary structure and active sites using the alignment of homologous sequences
inferredcites →https://doi.org/10.1016/0022-2836(88)90641-9openalex-snapshot
Helix geometry in proteins
inferredcites →https://doi.org/10.1016/0022-2836(89)90530-5openalex-snapshot
Structure and refinement of the oxidized P21 form of uteroglobin at 1.64 Å resolution
inferredcites →https://doi.org/10.1016/0022-4731(80)90019-9openalex-snapshot
Principles of protein structure
inferredcites →https://doi.org/10.1016/0065-2571(91)90012-bopenalex-snapshot
Patterns of divergence in homologous proteins as indicators of secondary and tertiary structure: A prediction of the structure of the catalytic domain of protein kinases
inferredcites →https://doi.org/10.1016/0167-4838(88)90206-3openalex-snapshot
Improvements in a secondary structure prediction method based on a search for local sequence homologies and its use as a model building tool
inferredcites →https://doi.org/10.1016/s0006-3495(98)77634-9openalex-snapshot
Geometrical and Sequence Characteristics of α-Helices in Globular Proteins
inferredcites →https://doi.org/10.1016/s0022-2836(05)80007-5openalex-snapshot
Redefining the goals of protein secondary structure prediction
inferredcites →https://doi.org/10.1016/s0022-2836(05)80333-xopenalex-snapshot
Machine learning approach for the prediction of protein secondary structure
inferredcites →https://doi.org/10.1016/s0022-2836(05)80360-2openalex-snapshot
Basic Local Alignment Search Tool
inferredcites →https://doi.org/10.1016/s0959-440x(94)90113-9openalex-snapshot
Classification of protein folds
inferredcites →https://doi.org/10.1016/s0968-0004(00)89105-7openalex-snapshot
Dali: a network tool for protein structure comparison
inferredcites →https://doi.org/10.1016/s0969-2126(97)00260-8openalex-snapshot
CATH – a hierarchic classification of protein domain structures
inferredcites →https://doi.org/10.1021/bi00571a023openalex-snapshot
Improvements in the prediction of protein backbone topography by reduction of statistical errors
inferredcites →https://doi.org/10.1021/bi00699a002openalex-snapshot
Prediction of protein conformation
inferredcites →https://doi.org/10.1038/11525openalex-snapshot
Identifying two ancient enzymes in Archaea using predicted secondary structure alignment.
inferredcites →https://doi.org/10.1073/pnas.070548997openalex-snapshot
Predicting protein function from structure: Unique structural features of proteases
inferredcites →https://doi.org/10.1073/pnas.85.8.2444openalex-snapshot
Improved tools for biological sequence comparison.
inferredcites →https://doi.org/10.1073/pnas.95.6.2818openalex-snapshot
Seeking an ancient enzyme in Methanococcus jannaschii using orf , a program based on predicted secondary structure comparisons
inferredcites →https://doi.org/10.1093/bioinformatics/14.10.892openalex-snapshot
JPred: a consensus secondary structure prediction server.
inferredcites →https://doi.org/10.1093/bioinformatics/15.9.759openalex-snapshot
Finding families for genomic ORFans
inferredcites →https://doi.org/10.1093/bioinformatics/17.1.63openalex-snapshot
What are the baselines for protein fold recognition?
inferredcites →https://doi.org/10.1093/nar/25.17.3389openalex-snapshot
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
inferredcites →https://doi.org/10.1093/nar/28.1.235openalex-snapshot
The Protein Data Bank
inferredcites →https://doi.org/10.1093/oso/9780199634972.003.0004openalex-snapshot
Prediction of secondary structure
inferredcites →https://doi.org/10.1093/protein/10.7.771openalex-snapshot
Exploring the limits of nearest neighbour secondary structure prediction
inferredcites →https://doi.org/10.1093/protein/13.1.15openalex-snapshot
Is it better to combine predictions?
inferredcites →https://doi.org/10.1093/protein/2.3.185openalex-snapshot
Secondary structure prediction: combination of three different methods
inferredcites →https://doi.org/10.1093/protein/6.4.377openalex-snapshot
Comparison of three algorithms for the assignment of secondary structure in proteins: the advantages of a consensus assignment
inferredcites →https://doi.org/10.1110/ps.31001openalex-snapshot
Effect of the N1 residue on the stability of the α‐helix for all 20 amino acids
inferredcites →https://doi.org/10.1110/ps.50701openalex-snapshot
Effect of the N2 residue on the stability of the α‐helix for all 20 amino acids
inferredcites →https://doi.org/10.1110/ps.8.10.2144openalex-snapshot
Position dependence of amino acid intrinsic helical propensities II: Non‐charged polar residues: Ser, Thr, Asn, and Gln
inferredcites →https://doi.org/10.1110/ps.9.6.1162openalex-snapshot
Cascaded multiple classifiers for secondary structure prediction
inferredcites →https://doi.org/10.1111/j.1399-3011.1982.tb02619.xopenalex-snapshot
Amino acid distribution in protein secondary structures
inferredcites →https://doi.org/10.1126/science.3381086openalex-snapshot
Amino Acid Preferences for Specific Locations at the Ends of α Helices

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Impact of Non-Proteinogenic Amino Acid Norvaline and Proteinogenic Valine Misincorporation on a Secondary Structure of a Model Peptide
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Improved prediction for N‐termini of α‐helices using empirical information
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Comprehensive analysis of the helix‐X‐helix motif in soluble proteins
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Impact of non-proteinogenic amino acid norvaline and proteinogenic valine misincorporation on a secondary structure of a model peptide
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Molecular Structure and Biochemical Properties of the HCCH−Zn2+ Site in HIV-1 Vif
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Synonymous codon usage influences the local protein structure observed
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Evolutionary computation for the prediction of secondary protein structures
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Protein secondary structures prediction based on evolutionary computation
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Impact of non-proteinogenic amino acid norvaline and proteinogenic valine misincorporation on a secondary structure of a model peptide
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