Results 41 to 50 of about 6,753,180 (197)

Percolation in protein sequence space. [PDF]

PLoS ONE, 2017
The currently known protein sequences are not distributed equally in sequence space, but cluster into families. Analyzing the cluster size distribution gives a glimpse of the large and unknown extant protein sequence space, which has been explored during
Patrick C F Buchholz, Silvia Fademrecht, Jürgen Pleiss   +2 more
doaj   +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   +2 more sources

An artificial immune system for clustering amino acids in the context of protein function classification [PDF]

, 2009
This paper addresses the classification task of data mining (a form of supervised learning) in the context of an important bioinformatics problem, namely the prediction of protein functions.
Timmis, Jon, Clark, Edward, Flower, Darren R., Secker, Andrew D., Davies, Matthew N., Freitas, Alex A.   +5 more
core   +1 more source

A Survey on Data Compression Methods for Biological Sequences

Information, 2016
The ever increasing growth of the production of high-throughput sequencing data poses a serious challenge to the storage, processing and transmission of these data. As frequently stated, it is a data deluge.
Morteza Hosseini, Diogo Pratas, Armando J. Pinho   +2 more
doaj   +1 more source

Predicting Protein–Protein Interactions Based on Ensemble Learning-Based Model from Protein Sequence

Biology, 2022
Protein–protein interactions (PPIs) play an essential role in many biological cellular functions. However, it is still tedious and time-consuming to identify protein–protein interactions through traditional experimental methods.
Xinke Zhan, Mang Xiao, Zhuhong You, Chenggang Yan, Jianxin Guo, Liping Wang, Yaoqi Sun, Bingwan Shang   +7 more
doaj   +1 more source

S2DA-GO: enhancing protein function prediction via gradient-decoupled cross-attention and semantic priors

Frontiers in Genetics
Accurate automated protein function prediction is essential for bridging the widening gap between the exponential accumulation of uncharacterized protein sequences and the limited repository of experimentally verified functional annotations.
Hailong Wang, Hailong Wang, Fujun Xiang, Fujun Xiang, Jin Zhang, Jin Zhang, Tingjie Wu, Tingjie Wu, Dong Wang, Dong Wang, Dong Wang, Dong Wang, Qiang Wang, Qiang Wang, Qiang Wang, Qiang Wang, Bin Lu, Bin Lu, Bin Lu, Bin Lu, Feifei Fu, Feifei Fu, Feifei Fu, Feifei Fu   +23 more
doaj   +1 more source

PredPSD: A Gradient Tree Boosting Approach for Single-Stranded and Double-Stranded DNA Binding Protein Prediction

Molecules, 2019
Interactions between proteins and DNAs play essential roles in many biological processes. DNA binding proteins can be classified into two categories. Double-stranded DNA-binding proteins (DSBs) bind to double-stranded DNA and are involved in a series of ...
Changgeng Tan, Tong Wang, Wenyi Yang, Lei Deng   +3 more
doaj   +1 more source

Protein sequence randomness and sequence/structure correlations

Biophysical Journal, 1995
We investigated protein sequence/structure correlation by constructing a space of protein sequences, based on methods developed previously for constructing a space of protein structures. The space is constructed by using a representation of the amino acids as vectors of 10 property factors that encode almost all of their physical properties.
Rahman, R.S., Rackovsky, S.
openaire   +2 more sources

Protein-Ligand Interactions: Docking, Design and Conformation Change [PDF]

, 2003
Virtual ligand screening has proven to be a successful strategy in drug design. An in house-developed procedure (HierDock), a coarse grain docking method followed by a fine grain search procedure, was used to determine the binding site for sugars in the
Datta, Deepshikha
core   +1 more source

Using sound to understand protein sequence data: new sonification algorithms for protein sequences and multiple sequence alignments

BMC Bioinformatics, 2021
Background The use of sound to represent sequence data—sonification—has great potential as an alternative and complement to visual representation, exploiting features of human psychoacoustic intuitions to convey nuance more effectively.
Edward J. Martin, Thomas R. Meagher, Daniel Barker   +2 more
doaj   +1 more source