Results 41 to 50 of about 1,014,642 (191)

An evolutionary method for learning HMM structure: prediction of protein secondary structure

BMC Bioinformatics, 2007
Background The prediction of the secondary structure of proteins is one of the most studied problems in bioinformatics. Despite their success in many problems of biological sequence analysis, Hidden Markov Models (HMMs) have not been used much for this ...
Won Kyoung-Jae, Hamelryck Thomas, Prügel-Bennett Adam, Krogh Anders   +3 more
doaj   +1 more source

Sulfur-mediated chalcogen versus hydrogen bonds in proteins: a see-saw effect in the conformational space

QRB Discovery, 2023
Divalent sulfur (S) forms a chalcogen bond (Ch-bond) via its σ-holes and a hydrogen bond (H-bond) via its lone pairs. The relevance of these interactions and their interplay for protein structure and function is unclear.
Vishal Annasaheb Adhav, Sanket Satish Shelke, Pananghat Balanarayan, Kayarat Saikrishnan   +3 more
doaj   +1 more source

FLORA: a novel method to predict protein function from structure in diverse superfamilies [PDF]

, 2009
Predicting protein function from structure remains an active area of interest, particularly for the structural genomics initiatives where a substantial number of structures are initially solved with little or no functional characterisation.
Dallman Timothy J., Nussinov, R., Oliver C. Redfern, Christine A. Orengo, Sillitoe, I., Dessailly Benoît H., Orengo, C.A., Benoît H Dessailly, Redfern, OC, Timothy J. Dallman, Oliver C Redfern, Benoît H. Dessailly, Dallman, TJ, Dessailly, B.H., Orengo Christine A., Ian Sillitoe, Timothy J Dallman, Sillitoe, I, Redfern Oliver C., Christine A Orengo, Dallman, T.J., Sillitoe Ian, Dessailly, BH, Redfern, O.C., Orengo, CA   +24 more
core   +1 more source

Secondary structure specific simpler prediction models for protein backbone angles [PDF]

, 2022
MOTIVATION: Protein backbone angle prediction has achieved significant accuracy improvement with the development of deep learning methods. Usually the same deep learning model is used in making prediction for all residues regardless of the categories of ...
Newton, MA Hakim, Sattar, Abdul, Zaman, Rianon, Mataeimoghadam, Fereshteh   +3 more
core   +1 more source

TMPSS: A Deep Learning-Based Predictor for Secondary Structure and Topology Structure Prediction of Alpha-Helical Transmembrane Proteins

Frontiers in Bioengineering and Biotechnology, 2021
Alpha transmembrane proteins (αTMPs) profoundly affect many critical biological processes and are major drug targets due to their pivotal protein functions.
Zhe Liu, Zhe Liu, Yingli Gong, Yihang Bao, Yuanzhao Guo, Han Wang, Guan Ning Lin, Guan Ning Lin   +7 more
doaj   +1 more source

SPIDER2: A Package to Predict Secondary Structure, Accessible Surface Area, and Main-Chain Torsional Angles by Deep Neural Networks [PDF]

, 2016
Predicting one-dimensional structure properties has played an important role to improve prediction of protein three-dimensional structures and functions.
Wang, Jihua, Lyons, James, Zhou, Yaoqi, Yaoqi Zhou, Paliwal, Kuldip, Kuldip Paliwal, Yuedong Yang, Rhys Heffernan, Dehzangi, Abdollah, Sattar, Abdul, Abdollah Dehzangi, Abdul Sattar, Heffernan, Rhys, James Lyons, Sharma, Alok, Alok Sharma, Yang, Yuedong, Jihua Wang   +17 more
core   +1 more source

Prediction of protein secondary structure content [PDF]

Protein Engineering, Design and Selection, 1999
All existing algorithms for predicting the content of protein secondary structure elements have been based on the conventional amino-acid-composition, where no sequence coupling effects are taken into account. In this article, an algorithm was developed for predicting the content of protein secondary structure elements that was based on a new amino ...
W, Liu, K C, Chou
openaire   +2 more sources

Rapid Quantification of Protein Secondary Structure Composition from a Single Unassigned 1D 13C NMR Spectrum [PDF]

The function of a protein is predicated upon its three dimensional fold. Representing its complex structure as a series of repeating secondary structural elements is one of the most useful ways by which we study, characterize, and visualize a protein ...
Haote, Li, Victor, Batista, Kurt, Zilm, Marcus, Tuttle   +3 more
core   +1 more source

Alignment of helical membrane protein sequences using AlignMe [PDF]

, 2013
Few sequence alignment methods have been designed specifically for integral membrane proteins, even though these important proteins have distinct evolutionary and structural properties that might affect their alignments.
René Staritzbichler, Stamm, Marcus, Staritzbichler, René, Khafizov, Kamil, Marcus Stamm (384964), Khafizov, K., Kamil Khafizov, Lucy R Forrest, René Staritzbichler (2667769), Staritzbichler, R., Marcus Stamm, Forrest, L., Forrest, Lucy R., Stamm, M., Kamil Khafizov (384965), Lucy R. Forrest (384966)   +15 more
core   +1 more source

Fourier Analysis of Conservation Patterns in Protein Secondary Structure

Computational and Structural Biotechnology Journal, 2017
Residue conservation is a common observation in alignments of protein families, underscoring positions important in protein structure and function. Though many methods measure the level of conservation of particular residue positions, currently we do not
Ashok Palaniappan, Eric Jakobsson
doaj   +1 more source