APID database: redefining proteinprotein interaction experimental evidences and binary interactomes

D Alonso-López, FJ Campos-Laborie, MA Gutiérrez… - Database, 2019 - academic.oup.com
… is high, especially in the case of human and yeast (over 90%). The generation and … PPIs
that these two resources have in common. This analysis reveals several important observations: …

A survey on computational models for predicting proteinprotein interactions

L Hu, X Wang, YA Huang, P Hu… - Briefings in …, 2021 - academic.oup.com
data and the other is integrated models that consider the biological information of proteins
extracted from different sources. … a theoretical and systematic analysis on how to perform the …

Reliable identification of protein-protein interactions by crosslinking mass spectrometry

S Lenz, LR Sinn, FJ O'Reilly, L Fischer… - Nature …, 2021 - nature.com
Source data are provided as a Source Data file. c Schematic … fraction may be crosslinked
in this analysis. In contrast, … PPI that includes a human or yeast protein is false. According to …

Discovering cellular proteinprotein interactions: Technological strategies and opportunities

K Titeca, I Lemmens, J Tavernier… - Mass spectrometry …, 2019 - Wiley Online Library
… ,3, 4 comprehensive analysis is challenging but central to our … On the one hand, iMYTH is
useful for original yeast proteins with … Another source of potential elimination of false positives …

Proteinprotein interaction sites prediction by ensemble random forests with synthetic minority oversampling technique

X Wang, B Yu, A Ma, C Chen, B Liu, Q Ma - Bioinformatics, 2019 - academic.oup.com
… sequence information of protein than the feature vectors obtained from the … different feature
extraction methods on the results, the robustness of feature extraction algorithms was derived

Comprehensive characterization of proteinprotein interactions perturbed by disease mutations

F Cheng, J Zhao, Y Wang, W Lu, Z Liu, Y Zhou… - Nature …, 2021 - nature.com
interaction perturbations caused by somatic mutations may contribute to tumorigenesis.
Following this analysis, … were then extracted, purified and transformed into Y8930 yeast strain for …

Predicting protein-protein interactions from matrix-based protein sequence using convolution neural network and feature-selective rotation forest

L Wang, HF Wang, SR Liu, X Yan, KJ Song - Scientific reports, 2019 - nature.com
… horizontal comparison that the results obtained by our model … than the other methods, but
the results obtained on the Yeast … two-hybrid analysis to explore the yeast protein interactome. …

BIPSPI: a method for the prediction of partner-specific proteinprotein interfaces

R Sanchez-Garcia, COS Sorzano, JM Carazo… - …, 2019 - academic.oup.com
… To avoid any effect or artefact due overtraining, we analyzed the scores obtained in the
leave-one-out cross-validation computed on DBv5 and DImS (see Section 3.2). Then, for each …

Yeast two‐hybrid assay to identify interacting proteins

A Paiano, A Margiotta, M De Luca… - … protocols in protein …, 2019 - Wiley Online Library
… the yeast clones isolated from the interaction screening or on the yeast colonies obtained
after … These approaches allow the identification and analysis of different types of interactions, …

IID 2018 update: context-specific physical proteinprotein interactions in human, model organisms and domesticated species

M Kotlyar, C Pastrello, Z Malik… - Nucleic acids research, 2019 - academic.oup.com
interactions were available only for human and yeast. … types of network analysis: topology
analysis to identify important … interaction sources. It specifies context by using ontologies and …