Macromolecular modeling and design in Rosetta: recent methods and frameworks

JK Leman, BD Weitzner, SM Lewis, J Adolf-Bryfogle… - Nature …, 2020 - nature.com
The Rosetta software for macromolecular modeling, docking and design is extensively used
in laboratories worldwide. During two decades of development by a community of …

[HTML][HTML] FoldX as protein engineering tool: better than random based approaches?

O Buß, J Rudat, K Ochsenreither - Computational and structural …, 2018 - Elsevier
Improving protein stability is an important goal for basic research as well as for clinical and
industrial applications but no commonly accepted and widely used strategy for efficient …

[HTML][HTML] Genomic and molecular landscape of DNA damage repair deficiency across the cancer genome atlas

TA Knijnenburg, L Wang, MT Zimmermann… - Cell reports, 2018 - cell.com
DNA damage repair (DDR) pathways modulate cancer risk, progression, and therapeutic
response. We systematically analyzed somatic alterations to provide a comprehensive view …

[HTML][HTML] Can predicted protein 3D structures provide reliable insights into whether missense variants are disease associated?

S Ittisoponpisan, SA Islam, T Khanna, E Alhuzimi… - Journal of molecular …, 2019 - Elsevier
Abstract Knowledge of protein structure can be used to predict the phenotypic consequence
of a missense variant. Since structural coverage of the human proteome can be roughly …

FoldX 5.0: working with RNA, small molecules and a new graphical interface

J Delgado, LG Radusky, D Cianferoni… - Bioinformatics, 2019 - academic.oup.com
A new version of FoldX, whose main new features allows running classic FoldX commands
on structures containing RNA molecules and includes a module that allows parametrization …

Protein structure analysis of the interactions between SARS-CoV-2 spike protein and the human ACE2 receptor: from conformational changes to novel neutralizing …

I Mercurio, V Tragni, F Busto, A De Grassi… - Cellular and Molecular …, 2021 - Springer
The recent severe acute respiratory syndrome, known as Coronavirus Disease 2019
(COVID-19) has spread so much rapidly and severely to induce World Health Organization …

Interactions of different polyphenols with bovine serum albumin using fluorescence quenching and molecular docking

M Skrt, E Benedik, Č Podlipnik, NP Ulrih - Food chemistry, 2012 - Elsevier
Polyphenols are responsible for the major organoleptic characteristics of plant-derived foods
and beverages. Here, we investigated the binding of several polyphenols to bovine serum …

Structure-and sequence-analysis inspired engineering of proteins for enhanced thermostability

HJ Wijma, RJ Floor, DB Janssen - Current opinion in structural biology, 2013 - Elsevier
Highlights•Targeting critical sites for stability improvement.•Consensus/ancestral sequence
based protein stabilization.•Computational design of thermostability.•Loop grafting and …

Mutations in KLHL40 are a frequent cause of severe autosomal-recessive nemaline myopathy

G Ravenscroft, S Miyatake, VL Lehtokari… - The American Journal of …, 2013 - cell.com
Nemaline myopathy (NEM) is a common congenital myopathy. At the very severe end of the
NEM clinical spectrum are genetically unresolved cases of autosomal-recessive fetal …

Enzyme hydration determines resistance in organic cosolvents

H Cui, L Zhang, L Eltoukhy, Q Jiang, SK Korkunç… - ACS …, 2020 - ACS Publications
Biocatalysis in organic solvents (OSs) has found various important applications, particularly
in organic synthesis and for the production of pharmaceuticals, flavors, and fragrances …