Computational prediction of RNA-binding proteins and binding sites

J Si, J Cui, J Cheng, R Wu - International journal of molecular sciences, 2015 - mdpi.com
Proteins and RNA interaction have vital roles in many cellular processes such as protein
synthesis, sequence encoding, RNA transfer, and gene regulation at the transcriptional and …

Prediction of Ubiquitination Sites by Using the Composition of k-Spaced Amino Acid Pairs

Z Chen, YZ Chen, XF Wang, C Wang, RX Yan… - PloS one, 2011 - journals.plos.org
As one of the most important reversible protein post-translation modifications, ubiquitination
has been reported to be involved in lots of biological processes and closely implicated with …

Target based drug design-a reality in virtual sphere

S Verma, Y S. Prabhakar - Current medicinal chemistry, 2015 - benthamdirect.com
The target based drug design approaches are a series of computational procedures,
including visualization tools, to support the decision systems of drug design/discovery …

RBPPred: predicting RNA-binding proteins from sequence using SVM

X Zhang, S Liu - Bioinformatics, 2017 - academic.oup.com
Motivation Detection of RNA-binding proteins (RBPs) is essential since the RNA-binding
proteins play critical roles in post-transcriptional regulation and have diverse roles in various …

ET-GRU: using multi-layer gated recurrent units to identify electron transport proteins

NQK Le, EKY Yapp, HY Yeh - BMC bioinformatics, 2019 - Springer
Background Electron transport chain is a series of protein complexes embedded in the
process of cellular respiration, which is an important process to transfer electrons and other …

Computational Identification of Protein Pupylation Sites by Using Profile-Based Composition of k-Spaced Amino Acid Pairs

MM Hasan, Y Zhou, X Lu, J Li, J Song, Z Zhang - PloS one, 2015 - journals.plos.org
Prokaryotic proteins are regulated by pupylation, a type of post-translational modification
that contributes to cellular function in bacterial organisms. In pupylation process, the …

Insights into the fold organization of TIM barrel from interaction energy based structure networks

MS Vijayabaskar, S Vishveshwara - PLoS computational biology, 2012 - journals.plos.org
There are many well-known examples of proteins with low sequence similarity, adopting the
same structural fold. This aspect of sequence-structure relationship has been extensively …

EPuL: an enhanced positive-unlabeled learning algorithm for the prediction of pupylation sites

X Nan, L Bao, X Zhao, X Zhao, AK Sangaiah, GG Wang… - Molecules, 2017 - mdpi.com
Protein pupylation is a type of post-translation modification, which plays a crucial role in
cellular function of bacterial organisms in prokaryotes. To have a better insight of the …

Structure prediction and network analysis of chitinases from the Cape sundew, Drosera capensis

MH Unhelkar, VT Duong, KN Enendu, JE Kelly… - … et Biophysica Acta (BBA …, 2017 - Elsevier
Background Carnivorous plants possess diverse sets of enzymes with novel functionalities
applicable to biotechnology, proteomics, and bioanalytical research. Chitinases constitute …

Outer membrane proteins can be simply identified using secondary structure element alignment

RX Yan, Z Chen, Z Zhang - BMC bioinformatics, 2011 - Springer
Abstract Background Outer membrane proteins (OMPs) are frequently found in the outer
membranes of gram-negative bacteria, mitochondria and chloroplasts and have been found …