Data driven flexible backbone protein design

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

(2016) Haiyan Liu et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

(2013) Sander Pronk et al.   BIOINFORMATICS

Computational design of protein–protein interactions

(2013) Gideon Schreiber et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

(2013) Mark A. Hallen et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

A Strategy for Modulation of Enzymes in the Ubiquitin System

(2013) A. Ernst et al.   SCIENCE

Determination of structural fluctuations of proteins from structure-based calculations of residual dipolar couplings

(2012) Rinaldo W. Montalvao et al.   JOURNAL OF BIOMOLECULAR NMR

Structural biology and drug discovery for protein–protein interactions

(2012) Harry Jubb et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

Polyubiquitin binding and cross-reactivity in the USP domain deubiquitinase USP21

(2011) Yu Ye et al.   EMBO REPORTS

Introduction to current and future protein therapeutics: A protein engineering perspective

(2011) Paul J. Carter   EXPERIMENTAL CELL RESEARCH

The FALC-Loop web server for protein loop modeling

(2011) J. Ko et al.   NUCLEIC ACIDS RESEARCH

Predicting the Tolerated Sequences for Proteins and Protein Interfaces Using RosettaBackrub Flexible Backbone Design

(2011) Colin A. Smith et al.   PLoS One

Computational Design of Proteins Targeting the Conserved Stem Region of Influenza Hemagglutinin

(2011) S. J. Fleishman et al.   SCIENCE

Phage display: Concept, innovations, applications and future

(2010) Jyoti Pande et al.   BIOTECHNOLOGY ADVANCES

Will the Ubiquitin System Furnish as Many Drug Targets as Protein Kinases?

(2010) Philip Cohen et al.   CELL

Ubiquitin-specific Peptidase 21 Inhibits Tumor Necrosis Factor α-induced Nuclear Factor κB Activation via Binding to and Deubiquitinating Receptor-interacting Protein 1

(2009) Gufeng Xu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Protein Design by Directed Evolution

(2008) Christian Jäckel et al.   Annual Review of Biophysics

The minimized dead-end elimination criterion and its application to protein redesign in a hybrid scoring and search algorithm for computing partition functions over molecular ensembles

(2008) Ivelin Georgiev et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

A Simple Model of Backbone Flexibility Improves Modeling of Side-chain Conformational Variability

(2008) Gregory D. Friedland et al.   JOURNAL OF MOLECULAR BIOLOGY

Backrub-Like Backbone Simulation Recapitulates Natural Protein Conformational Variability and Improves Mutant Side-Chain Prediction

(2008) Colin A. Smith et al.   JOURNAL OF MOLECULAR BIOLOGY