Predicting protein–protein interactions from the molecular to the proteome level
Identification of protein–protein interactions (PPIs) is at the center of molecular biology
considering the unquestionable role of proteins in cells. Combinatorial interactions result in …
considering the unquestionable role of proteins in cells. Combinatorial interactions result in …
Protein–RNA interaction prediction with deep learning: structure matters
Protein–RNA interactions are of vital importance to a variety of cellular activities. Both
experimental and computational techniques have been developed to study the interactions …
experimental and computational techniques have been developed to study the interactions …
Predicting membrane protein types by incorporating protein topology, domains, signal peptides, and physicochemical properties into the general form of Chou's …
YK Chen, KB Li - Journal of Theoretical Biology, 2013 - Elsevier
The type information of un-annotated membrane proteins provides an important hint for their
biological functions. The experimental determination of membrane protein types, despite …
biological functions. The experimental determination of membrane protein types, despite …
Redefining the specificity of phosphoinositide-binding by human PH domain-containing proteins
N Singh, A Reyes-Ordoñez, MA Compagnone… - Nature …, 2021 - nature.com
Pleckstrin homology (PH) domains are presumed to bind phosphoinositides (PIPs), but
specific interaction with and regulation by PIPs for most PH domain-containing proteins are …
specific interaction with and regulation by PIPs for most PH domain-containing proteins are …
Computational methods for prediction of protein–RNA interactions
T Puton, L Kozlowski, I Tuszynska, K Rother… - Journal of structural …, 2012 - Elsevier
Understanding the molecular mechanism of protein–RNA recognition and complex
formation is a major challenge in structural biology. Unfortunately, the experimental …
formation is a major challenge in structural biology. Unfortunately, the experimental …
The rough guide to in silico function prediction, or how to use sequence and structure information to predict protein function
Choosing the right function prediction tools. The vast majority of known proteins have not yet
been characterized experimentally, and there is very little that is known about their function …
been characterized experimentally, and there is very little that is known about their function …
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 …
synthesis, sequence encoding, RNA transfer, and gene regulation at the transcriptional and …
An overview of the prediction of protein DNA-binding sites
J Si, R Zhao, R Wu - International journal of molecular sciences, 2015 - mdpi.com
Interactions between proteins and DNA play an important role in many essential biological
processes such as DNA replication, transcription, splicing, and repair. The identification of …
processes such as DNA replication, transcription, splicing, and repair. The identification of …
PEP-patch: electrostatics in protein–protein recognition, specificity, and antibody developability
The electrostatic properties of proteins arise from the number and distribution of polar and
charged residues. Electrostatic interactions in proteins play a critical role in numerous …
charged residues. Electrostatic interactions in proteins play a critical role in numerous …
Molecular insights into the interaction between human nicotinamide phosphoribosyltransferase and Toll-like receptor 4
The secreted form of the enzyme nicotinamide phosphoribosyltransferase (NAMPT), which
catalyzes a key reaction in intracellular NAD biosynthesis, acts as a damage-associated …
catalyzes a key reaction in intracellular NAD biosynthesis, acts as a damage-associated …