De novo design of a four-fold symmetric TIM-barrel protein with atomic-level accuracy

Design of symmetric TIM barrel proteins from first principles

(2015) Deepesh Nagarajan et al.   BMC BIOCHEMISTRY

A General Computational Approach for Repeat Protein Design

(2015) Fabio Parmeggiani et al.   JOURNAL OF MOLECULAR BIOLOGY

Reversibility and two state behaviour in the thermal unfolding of oligomeric TIM barrel proteins

(2015) Sergio Romero-Romero et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Proof of principle for epitope-focused vaccine design

(2014) Bruno E. Correia et al.   NATURE

Evolutionary relationship of two ancient protein superfolds

(2014) José Arcadio Farías-Rico et al.   Nature Chemical Biology

Computational design of a leucine-rich repeat protein with a predefined geometry

(2014) Sebastian Rämisch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

De novo design of a transmembrane Zn2+-transporting four-helix bundle

(2014) Nathan H. Joh et al.   SCIENCE

High thermodynamic stability of parametrically designed helical bundles

(2014) Po-Ssu Huang et al.   SCIENCE

De Novo Design and Experimental Characterization of Ultrashort Self-Associating Peptides

(2014) James Smadbeck et al.   PLoS Computational Biology

Computational Enzyme Design

(2013) Gert Kiss et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

MICAN : a protein structure alignment algorithm that can handle Multiple-chains, Inverse alignments, Cα only models, Alternative alignments, and Non-sequential alignments

(2013) Shintaro Minami et al.   BMC BIOINFORMATICS

Evolution of a designed retro-aldolase leads to complete active site remodeling

(2013) Lars Giger et al.   Nature Chemical Biology

Improved low-resolution crystallographic refinement with Phenix and Rosetta

(2013) Frank DiMaio et al.   NATURE METHODS

Octarellin VI: Using Rosetta to Design a Putative Artificial (β/α)8 Protein

(2013) Maximiliano Figueroa et al.   PLoS One

High-Resolution Comparative Modeling with RosettaCM

(2013) Yifan Song et al.   STRUCTURE

Protein folding and de novo protein design for biotechnological applications

(2013) George A. Khoury et al.   TRENDS IN BIOTECHNOLOGY

Towards automated crystallographic structure refinement withphenix.refine

(2012) Pavel V. Afonine et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

De Novo Peptide Design with C3a Receptor Agonist and Antagonist Activities: Theoretical Predictions and Experimental Validation

(2012) Meghan L. Bellows-Peterson et al.   JOURNAL OF MEDICINAL CHEMISTRY

Principles for designing ideal protein structures

(2012) Nobuyasu Koga et al.   NATURE

Exploring the Structure–Function Loop Adaptability of a (β/α)8-Barrel Enzyme through Loop Swapping and Hinge Variability

(2011) Adrián Ochoa-Leyva et al.   JOURNAL OF MOLECULAR BIOLOGY

Exploring Symmetry as an Avenue to the Computational Design of Large Protein Domains

(2011) Carie Fortenberry et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment

(2011) Michael Remmert et al.   NATURE METHODS

RosettaRemodel: A Generalized Framework for Flexible Backbone Protein Design

(2011) Po-Ssu Huang et al.   PLoS One

Characteristics of a de novo designed protein

(2010) Toshiki Tanaka et al.   PROTEIN SCIENCE

High-Resolution Crystal Structure of an Artificial (βα)8-Barrel Protein Designed from Identical Half-Barrels†‡

(2009) Birte Höcker et al.   BIOCHEMISTRY

Protein Design through Systematic Catalytic Loop Exchange in the (β/α)8 Fold

(2009) Adrián Ochoa-Leyva et al.   JOURNAL OF MOLECULAR BIOLOGY

βα-Hairpin Clamps Brace βαβ Modules and Can Make Substantive Contributions to the Stability of TIM Barrel Proteins

(2009) Xiaoyan Yang et al.   PLoS One

Establishing wild-type levels of catalytic activity on natural and artificial (  )8-barrel protein scaffolds

(2009) J. Claren et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA