Theoretical and computational protein design

I Samish, CM MacDermaid… - Annual review of …, 2011 - annualreviews.org
From exponentially large numbers of possible sequences, protein design seeks to identify
the properties of those that fold to predetermined structures and have targeted structural and …

[HTML][HTML] In silico methods for design of biological therapeutics

A Roy, S Nair, N Sen, N Soni, MS Madhusudhan - Methods, 2017 - Elsevier
It has been twenty years since the first rationally designed small molecule drug was
introduced into the market. Since then, we have progressed from designing small molecules …

Rational design of a ligand-controlled protein conformational switch

O Dagliyan, D Shirvanyants, A Karginov, F Ding… - Biophysical …, 2013 - cell.com
Results. Acute MI caused frequent ventricular ectopyduring the steady-state pacing, but not
after a pause. Acute MI hearts became susceptible to postpause ectopy only after Ca2þ …

Dead‐end elimination with perturbations (DEEPer): A provable protein design algorithm with continuous sidechain and backbone flexibility

MA Hallen, DA Keedy… - … : Structure, Function, and …, 2013 - Wiley Online Library
Computational protein and drug design generally require accurate modeling of protein
conformations. This modeling typically starts with an experimentally determined protein …

Multistate approaches in computational protein design

JA Davey, RA Chica - Protein Science, 2012 - Wiley Online Library
Computational protein design (CPD) is a useful tool for protein engineers. It has been
successfully applied towards the creation of proteins with increased thermostability …

Rosetta: MSF: a modular framework for multi-state computational protein design

P Löffler, S Schmitz, E Hupfeld, R Sterner… - PLoS computational …, 2017 - journals.plos.org
Computational protein design (CPD) is a powerful technique to engineer existing proteins or
to design novel ones that display desired properties. Rosetta is a software suite including …

Physics-based computational protein design: an update

D Mignon, K Druart, E Michael, V Opuu… - The Journal of …, 2020 - ACS Publications
We describe methods for physics-based protein design and some recent applications from
our work. We present the physical interpretation of a MC simulation in sequence space and …

Algorithm for backrub motions in protein design

I Georgiev, D Keedy, JS Richardson… - …, 2008 - academic.oup.com
Abstract Motivation: The Backrub is a small but kinematically efficient side-chain-coupled
local backbone motion frequently observed in atomic-resolution crystal structures of …

Computationally optimized deimmunization libraries yield highly mutated enzymes with low immunogenicity and enhanced activity

RS Salvat, D Verma, AS Parker… - Proceedings of the …, 2017 - National Acad Sciences
Therapeutic proteins of wide-ranging function hold great promise for treating disease, but
immune surveillance of these macromolecules can drive an antidrug immune response that …

Design of protein multi-specificity using an independent sequence search reduces the barrier to low energy sequences

AM Sevy, TM Jacobs, JE Crowe Jr… - PLoS computational …, 2015 - journals.plos.org
Computational protein design has found great success in engineering proteins for
thermodynamic stability, binding specificity, or enzymatic activity in a 'single state'design …