Computational protein design for given backbone: recent progresses in general method-related aspects

H Liu, Q Chen - Current opinion in structural biology, 2016 - Elsevier
… In different protein design tasks, it is often common requisites … interactions in failed
proteinprotein interface designs, while … between inter-solute hydrogen bonding and desolvation …

Automated protein design: Landmarks and operational principles

A Kumar, R Ranbhor, K Patel, V Ramakrishnan… - Progress in biophysics …, 2017 - Elsevier
… locked in inter-residual hydrogen bonding network, with α -… module of DNA binding protein
Zif268 highlighting the residues (… burial benefit and a polar-burial penalty in the protein-design

De novo design of modular and tunable protein biosensors

A Quijano-Rubio, HW Yeh, J Park, H Lee, RA Langan… - Nature, 2021 - nature.com
buried polar interactions at the cage–latch or cage–key … results highlight the potential of de
novo protein design to … Unless otherwise indicated, data are shown as mean ± sd, and error

[PDF][PDF] Fast and flexible protein design using deep graph neural networks

A Strokach, D Becerra, C Corbi-Verge, A Perez-Riba… - Cell systems, 2020 - cell.com
… In order to facilitate this search, we focused on designing a … ), or residues that are buried in
the protein core (purple). The … Although this made its characterization challenging, we were …

Protein–small molecule interactions in native mass spectrometry

JL Bennett, GTH Nguyen, WA Donald - Chemical Reviews, 2021 - ACS Publications
highlight some of the key areas in modern drug design for … , for which most basic residues
were buried and not accessible for … ionic interactions and neutral hydrogen bonds can stabilize …

Computational tools applied to enzyme design− a review

F García-Guevara, M Avelar, M Ayala, L Segovia - Biocatalysis, 2016 - degruyter.com
… ), highlighting its predictive power for ranking designs during … of different interactions (hydrogen
bonds, electrostatic and … ) a more buried catalytic residue (7 Å deeper into the protein

Achievements and challenges in computational protein design

I Samish - Computational Protein Design, 2017 - Springer
… that buried and interfacial hydrogen bonds are pivotal for oligomerization. … This study
highlights the need to carefully design the … science highlights success stories rather than failures. …

[图书][B] Learning How to Make Mini-Proteins that Bind to Specific Target Proteins

B Coventry - 2021 - search.proquest.com
… state it would be making a hydrogen bond. We will refer to such atoms as buried unsats. …
Plotted is the error in recovery when 3BOP was enabled. The general trend is that the more …

Two strategies to engineer flexible loops for improved enzyme thermostability

H Yu, Y Yan, C Zhang, PA Dalby - Scientific reports, 2017 - nature.com
… the protein surface, whereas loops deeply buried in the protein … This highlights both the
powerful capability of Rosetta in … number of hydrogen bonds revealed differences for specific …

De novo design of bioactive protein switches

RA Langan, SE Boyken, AH Ng, JA Samson, G Dods… - Nature, 2019 - nature.com
protein function is widespread in biology, but is challenging … to design interfaces containing
buried hydrogen-bond networks; … cells, which highlights the modularity and utility of LOCKR. …