Protein design: From the aspect of water solubility and stability

R Qing, S Hao, E Smorodina, D **, A Zalevsky… - Chemical …, 2022 - ACS Publications
Water solubility and structural stability are key merits for proteins defined by the primary
sequence and 3D-conformation. Their manipulation represents important aspects of 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 …

PremPS: Predicting the impact of missense mutations on protein stability

Y Chen, H Lu, N Zhang, Z Zhu, S Wang… - PLoS computational …, 2020 - journals.plos.org
Computational methods that predict protein stability changes induced by missense
mutations have made a lot of progress over the past decades. Most of the available methods …

A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions

MV Shapovalov, RL Dunbrack - Structure, 2011 - cell.com
Rotamer libraries are used in protein structure determination, prediction, and design. The
backbone-dependent rotamer library consists of rotamer frequencies, mean dihedral angles …

BeAtMuSiC: prediction of changes in protein–protein binding affinity on mutations

Y Dehouck, JM Kwasigroch, M Rooman… - Nucleic acids …, 2013 - academic.oup.com
The ability of proteins to establish highly selective interactions with a variety of (macro)
molecular partners is a crucial prerequisite to the realization of their biological functions. The …

Enhancing antibody Fc heterodimer formation through electrostatic steering effects: applications to bispecific molecules and monovalent IgG

K Gunasekaran, M Pentony, M Shen, L Garrett… - Journal of Biological …, 2010 - jbc.org
Naturally occurring IgG antibodies are bivalent and monospecific. Bispecific antibodies
having binding specificities for two different antigens can be produced using recombinant …

Performance of protein stability predictors

S Khan, M Vihinen - Human mutation, 2010 - Wiley Online Library
Stability is a fundamental property affecting function, activity, and regulation of biomolecules.
Stability changes are often found for mutated proteins involved in diseases. Stability …

Protein design by directed evolution

C Jäckel, P Kast, D Hilvert - Annu. Rev. Biophys., 2008 - annualreviews.org
While nature evolved polypeptides over billions of years, protein design by evolutionary
mimicry is progressing at a far more rapid pace. The mutation, selection, and amplification …

Assessing computational methods for predicting protein stability upon mutation: good on average but not in the details

V Potapov, M Cohen, G Schreiber - Protein engineering, design …, 2009 - academic.oup.com
Methods for protein modeling and design advanced rapidly in recent years. At the heart of
these computational methods is an energy function that calculates the free energy of the …

Prediction of protein mutational free energy: benchmark and sampling improvements increase classification accuracy

B Frenz, SM Lewis, I King, F DiMaio, H Park… - … in bioengineering and …, 2020 - frontiersin.org
Software to predict the change in protein stability upon point mutation is a valuable tool for a
number of biotechnological and scientific problems. To facilitate the development of such …