[PDF][PDF] X-ray Crystallographic Validation of Structure Predictions Used in Computational Protein Stabilization

RJ Floor, HJ Wijma, PA Jekel… - … protein engineering by … - research.rug.nl
High enzyme stability facilitates development of biocatalytic processes because of the
reduced catalyst inactivation, the increased solubility of substrates and products and the …

X‐ray crystallographic validation of structure predictions used in computational design for protein stabilization

RJ Floor, HJ Wijma, PA Jekel… - Proteins: Structure …, 2015 - Wiley Online Library
Protein engineering aimed at enhancing enzyme stability is increasingly supported by
computational methods for calculation of mutant folding energies and for the design of …

Efficient protein engineering by combining computational design and directed evolution

R Floor - 2015 - research.rug.nl
The use of enzymes in industrial catalysis can result in large environmental benefits.
Enzymes often have a high activity and specificity and thereby are able to convert raw …

Computationally designed libraries for rapid enzyme stabilization

HJ Wijma, RJ Floor, PA Jekel, D Baker… - … , Design & Selection, 2014 - academic.oup.com
The ability to engineer enzymes and other proteins to any desired stability would have wide-
ranging applications. Here, we demonstrate that computational design of a library with …

[PDF][PDF] Protein Structure Refinement with Adaptable Restraints

A Wildberg - 2013 - docserv.uni-duesseldorf.de
Proteins and especially their structures play an essential role in computational structural
biology. With accurate characterizations of proteins, processes like drug design and docking …

Large‐scale prediction of protein geometry and stability changes for arbitrary single point mutations

AJ Bordner, RA Abagyan - Proteins: Structure, Function, and …, 2004 - Wiley Online Library
We have developed a method to both predict the geometry and the relative stability of point
mutants that may be used for arbitrary mutations. The geometry optimization procedure was …

Conformation‐dependent backbone geometry restraints set a new standard for protein crystallographic refinement

NW Moriarty, DE Tronrud, PD Adams… - The FEBS …, 2014 - Wiley Online Library
Ideal values of bond angles and lengths used as external restraints are crucial for the
successful refinement of protein crystal structures at all but the highest of resolutions. The …

Quality assessment of the model

Z Dauter, GN Murshudov, KS Wilson - 2012 - Wiley Online Library
The refinement of proteins at resolutions lower than atomic depends upon the use of
restraints on the geometry and ADPs. The almost exclusively used library of target geometric …

Structure refinement of protein model decoys requires accurate side‐chain placement

MA Olson, MS Lee - Proteins: Structure, Function, and …, 2013 - Wiley Online Library
In this study, the application of temperature‐based replica‐exchange (T‐ReX) simulations
for structure refinement of decoys taken from the I‐TASSER dataset was examined. A set of …

Strategy for supplementing structure calculations using limited data with hydrophobic distance restraints

AT Alexandrescu - Proteins: Structure, Function, and …, 2004 - Wiley Online Library
Introductory biochemistry texts often note that the fold of a protein is completely defined
when the dihedral angles ϕ and ψ are known for each amino acid. This assertion was …