Computational Prediction of Secondary and Supersecondary Structures from Protein Sequences

Oldfield, Christopher J.; Chen, Ke; Kurgan, Lukasz

doi:10.1007/978-1-4939-9161-7_4

Cited by 11 publications

(8 citation statements)

References 174 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Secondary structure predictors are usually classified in three classes or “generations,” according to their theoretical basis and procedures (see refs. and for extensive reviews). First‐generation methods analyze individual propensities of amino acids on an almost purely statistical basis, whereas second‐generation procedures take into account the neighboring residues and carry out the prediction in sliding segments (windows) of amino acids.…”

Section: Chameleon Sequencesmentioning

confidence: 99%

Turncoat Polypeptides: We Adapt to Our Environment

et al. 2019

View full text Add to dashboard Cite

A common interpretation of Anfinsen's hypothesis states that one amino acid sequence should fold into a single, native, ordered state, or a highly similar set thereof, coinciding with the global minimum in the folding‐energy landscape, which, in turn, is responsible for the function of the protein. However, this classical view is challenged by many proteins and peptide sequences, which can adopt exchangeable, significantly dissimilar conformations that even fulfill different biological roles. The similarities and differences of concepts related to these proteins, mainly chameleon sequences, metamorphic proteins, and switch peptides, which are all denoted herein “turncoat” polypeptides, are reviewed. As well as adding a twist to the conventional view of protein folding, the lack of structural definition adds clear versatility to the activity of proteins and can be used as a tool for protein design and further application in biotechnology and biomedicine.

show abstract

Section: Chameleon Sequencesmentioning

confidence: 99%

Turncoat Polypeptides: We Adapt to Our Environment

et al. 2019

View full text Add to dashboard Cite

show abstract

“…The huge amount of protein sequences that lack the residue-level annotations has motivated the development of hundreds of computational methods that predict these annotations from the sequences. For instance, there are over 60 predictors of the secondary structure [5] , [6] , [7] , over 100 predictors of the intrinsic disorder [8] , [9] , [10] , [11] , [12] , and close to 40 predictors of the residues that bind nucleic acids [13] , [14] , [15] . Some of these methods are heavily used, which can be indirectly measured by their citations.…”

Section: Introductionmentioning

confidence: 99%

“…Availability of the many sequence-based predictors of the residue-level annotations has spurred numerous studies that survey and compare these tools [1] , [2] , [5] , [6] , [7] , [8] , [9] , [10] , [11] , [13] , [14] , [15] , [29] , [30] , [31] , [32] , [33] , [34] , [35] , [36] , [37] , [38] , [39] , [40] , [41] , [42] , [43] , [44] , [45] , [46] . A large portion of these studies focuses on the empirical comparative assessment of their predictive performance.…”

Section: Introductionmentioning

confidence: 99%

Complementarity of the residue-level protein function and structure predictions in human proteins

Biró

Zhao

Kurgan

2022

Computational and Structural Biotechnology Journal

Self Cite

View full text Add to dashboard Cite

“…[15] In the natural world, information is encoded within the amino acid sequence of proteins to direct their folding and therefore function (Figure 1A). [16] Such structure-activity relationships inspired ab ottom-up construction of functional [17] and cavity-containing [18] proteins,w hich is at the forefront of biochemistry research. [19] On the other hand, supramolecular chemists have approached this problem by creating sequence-defined foldamers [20] and chiral cavitands [21] for studying molecular encapsulation.…”

Section: Introductionmentioning

confidence: 99%

Enantioselective Construction of Modular and Asymmetric Baskets

et al. 2021

View full text Add to dashboard Cite

The precise positioning of functional groups about the inner space of abiotic hosts is ac hallenging task and of interest for developing more effective receptors and catalysts akin to those found in nature.T oa ddress it, we herein report as ynthetic methodology for preparing basket-like cavitands comprised of three different aromatics as side arms with orthogonal esters at the rim for further functionalization. First, enantioenriched A (borochloronorbornene), B (iodobromonorbornene), and C (boronorbornene) building blocks were obtained by stereoselective syntheses.S econd, consecutive Ato-B and then AB-to-C Suzuki-Miyaura (SM) couplings were optimizedt og ive enantioenriched ABC cavitand as the principal product. The robust synthetic protocol allowed us to prepare (a) an enantioenriched basket with three benzene sides and each holding either tBu, Et, or Me esters,( b) both enantiomers of as o-called "spiral staircase" basket with benzene, naphthalene,a nd anthracene groups surrounding the inner space,and (c) aphoto-responsive basket bearing one anthracene and two benzene arms.

show abstract

Computational Prediction of Secondary and Supersecondary Structures from Protein Sequences

Cited by 11 publications

References 174 publications

Turncoat Polypeptides: We Adapt to Our Environment

Turncoat Polypeptides: We Adapt to Our Environment

Complementarity of the residue-level protein function and structure predictions in human proteins

Enantioselective Construction of Modular and Asymmetric Baskets

Contact Info

Product

Resources

About