iProt-Sub: a comprehensive package for accurately mapping and predicting protease-specific substrates and cleavage sites

J Song, Y Wang, F Li, T Akutsu… - Briefings in …, 2019 - academic.oup.com
Regulation of proteolysis plays a critical role in a myriad of important cellular processes. The
key to better understanding the mechanisms that control this process is to identify the …

The state-of-the-art strategies of protein engineering for enzyme stabilization

Q Liu, G Xun, Y Feng - Biotechnology advances, 2019 - Elsevier
Enzymes generated by natural recruitment and protein engineering have greatly contribute
in various sets of applications. However, their insufficient stability is a bottleneck that limit the …

I-TASSER server: new development for protein structure and function predictions

J Yang, Y Zhang - Nucleic acids research, 2015 - academic.oup.com
The I-TASSER server (http://zhanglab. ccmb. med. umich. edu/I-TASSER) is an online
resource for automated protein structure prediction and structure-based function annotation …

Basic validation procedures for regression models in QSAR and QSPR studies: theory and application

R Kiralj, M Ferreira - Journal of the Brazilian Chemical Society, 2009 - SciELO Brasil
Four quantitative structure-activity relationships (QSAR) and quantitative structure-property
relationship (QSPR) data sets were selected from the literature and used to build regression …

Engineering proteins for thermostability through rigidifying flexible sites

H Yu, H Huang - Biotechnology advances, 2014 - Elsevier
Engineering proteins for thermostability is an exciting and challenging field since it is critical
for broadening the industrial use of recombinant proteins. Thermostability of proteins arises …

Engineering of flexible loops in enzymes

BM Nestl, B Hauer - Acs Catalysis, 2014 - ACS Publications
From a chemical point of view, enzymes are by far the most structurally complex and
functionally sophisticated molecules known. This is perhaps not surprising, once one …

Evolutionary dynamics of genome size and content during the adaptive radiation of Heliconiini butterflies

F Cicconardi, E Milanetti, EC Pinheiro de Castro… - Nature …, 2023 - nature.com
Heliconius butterflies, a speciose genus of Müllerian mimics, represent a classic example of
an adaptive radiation that includes a range of derived dietary, life history, physiological and …

Protein elastic network models and the ranges of cooperativity

L Yang, G Song, RL Jernigan - Proceedings of the National …, 2009 - National Acad Sciences
Elastic network models (ENMs) are entropic models that have demonstrated in many
previous studies their abilities to capture overall the important internal motions, with …

PREvaIL, an integrative approach for inferring catalytic residues using sequence, structural, and network features in a machine-learning framework

J Song, F Li, K Takemoto, G Haffari, T Akutsu… - Journal of theoretical …, 2018 - Elsevier
Determining the catalytic residues in an enzyme is critical to our understanding the
relationship between protein sequence, structure, function, and enhancing our ability to …

What makes a protein fold amenable to functional innovation? Fold polarity and stability trade-offs

E Dellus-Gur, A Toth-Petroczy, M Elias… - Journal of molecular …, 2013 - Elsevier
Protein evolvability includes two elements—robustness (or neutrality, mutations having no
effect) and innovability (mutations readily inducing new functions). How are these two …