Local protein structures

B Offmann, M Tyagi, AG de Brevern - Current Bioinformatics, 2007 - ingentaconnect.com
Protein structures are classically described as composed of two regular states, the α-helices
and the β-strands and one non-regular and variable state, the coil. Nonetheless, this simple …

[HTML][HTML] Determinants of antigenicity and specificity in immune response for protein sequences

Y Wang, W Wu, NN Negre, KP White, C Li, PK Shah - BMC bioinformatics, 2011 - Springer
Background Target specific antibodies are pivotal for the design of vaccines,
immunodiagnostic tests, studies on proteomics for cancer biomarker discovery, identification …

[HTML][HTML] Providencia alcalifaciens—Assisted Bioremediation of Chromium-Contaminated Groundwater: A Computational Study

M Tasleem, WM Hussein, AAAA El-Sayed, A Alrehaily - Water, 2023 - mdpi.com
In Saudi Arabia, seawater desalination is the primary source of acquiring freshwater, and
groundwater contains a high concentration of toxic heavy metals. Chromium (Cr) is one of …

Fold recognition by concurrent use of solvent accessibility and residue depth

S Liu, C Zhang, S Liang, Y Zhou - Proteins: Structure, Function …, 2007 - Wiley Online Library
Recognizing the structural similarity without significant sequence identity (called fold
recognition) is the key for bridging the gap between the number of known protein sequences …

Real‐SPINE: An integrated system of neural networks for real‐value prediction of protein structural properties

O Dor, Y Zhou - PROTEINS: Structure, Function, and …, 2007 - Wiley Online Library
Proteins can move freely in three‐dimensional space. As a result, their structural properties,
such as solvent accessible surface area, backbone dihedral angles, and atomic distances …

[HTML][HTML] Prediction of protein secondary structure based on an improved channel attention and multiscale convolution module

X Jin, L Guo, Q Jiang, N Wu, S Yao - Frontiers in Bioengineering and …, 2022 - frontiersin.org
Prediction of the protein secondary structure is a key issue in protein science. Protein
secondary structure prediction (PSSP) aims to construct a function that can map the amino …

Critical assessment of high-throughput standalone methods for secondary structure prediction

H Zhang, T Zhang, K Chen, KD Kedarisetti… - Briefings in …, 2011 - academic.oup.com
Sequence-based prediction of protein secondary structure (SS) enjoys wide-spread and
increasing use for the analysis and prediction of numerous structural and functional …

[HTML][HTML] A dynamic Bayesian network approach to protein secondary structure prediction

XQ Yao, H Zhu, ZS She - BMC bioinformatics, 2008 - Springer
Background Protein secondary structure prediction method based on probabilistic models
such as hidden Markov model (HMM) appeals to many because it provides meaningful …

Real‐value prediction of backbone torsion angles

B Xue, O Dor, E Faraggi, Y Zhou - Proteins: Structure, Function …, 2008 - Wiley Online Library
The backbone structure of a protein is largely determined by the ϕ and ψ torsion angles.
Thus, knowing these angles, even if approximately, will be very useful for protein‐structure …

[HTML][HTML] DDIG-in: discriminating between disease-associated and neutral non-frameshifting micro-indels

H Zhao, Y Yang, H Lin, X Zhang, M Mort, DN Cooper… - Genome biology, 2013 - Springer
Micro-indels (insertions or deletions shorter than 21 bps) constitute the second most
frequent class of human gene mutation after single nucleotide variants. Despite the relative …