Artificial Diiron Enzymes with a De Novo Designed Four-Helix Bundle Structure

Frag’r’Us: knowledge-based sampling of protein backbone conformations for de novo structure-based protein design

(2014) Jaume Bonet et al.   BIOINFORMATICS

Characterization of the N-oxygenase AurF from Streptomyces thioletus

(2014) Emmanuel Chanco et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Protein Design: Toward Functional Metalloenzymes

(2014) Fangting Yu et al.   CHEMICAL REVIEWS

Metalloenzyme design and engineering through strategic modifications of native protein scaffolds

(2014) Igor D Petrik et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Computational de novo design of a four-helix bundle protein-DND_4HB

(2014) Grant S. Murphy et al.   PROTEIN SCIENCE

A Real-Time All-Atom Structural Search Engine for Proteins

(2014) Gabriel Gonzalez et al.   PLoS Computational Biology

Energy Functions in De Novo Protein Design: Current Challenges and Future Prospects

(2013) Zhixiu Li et al.   Annual Review of Biophysics

Advances, Interactions, and Future Developments in the CNS, Phenix, and Rosetta Structural Biology Software Systems

(2013) Paul D. Adams et al.   Annual Review of Biophysics

Recurrent Structural Motifs in Non-Homologous Protein Structures

(2013) Maria Johansson et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

A Set of de Novo Designed Parallel Heterodimeric Coiled Coils with Quantified Dissociation Constants in the Micromolar to Sub-nanomolar Regime

(2013) Franziska Thomas et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

EvoDesign: de novo protein design based on structural and evolutionary profiles

(2013) Pralay Mitra et al.   NUCLEIC ACIDS RESEARCH

Structure of the trypanosome cyanide-insensitive alternative oxidase

(2013) T. Shiba et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Catalysis by a De Novo Zinc-Mediated Protein Interface: Implications for Natural Enzyme Evolution and Rational Enzyme Engineering

(2012) Bryan S. Der et al.   BIOCHEMISTRY

Defining and searching for structural motifs using DeepView/Swiss-PdbViewer

(2012) Maria U Johansson et al.   BMC BIOINFORMATICS

Principles for designing ideal protein structures

(2012) Nobuyasu Koga et al.   NATURE

Computational redesign of a mononuclear zinc metalloenzyme for organophosphate hydrolysis

(2012) Sagar D Khare et al.   Nature Chemical Biology

Alteration of the oxygen-dependent reactivity of de novo Due Ferri proteins

(2012) Amanda J. Reig et al.   Nature Chemistry

Computational design of a protein crystal

(2012) C. J. Lanci et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Basis Set of de Novo Coiled-Coil Peptide Oligomers for Rational Protein Design and Synthetic Biology

(2012) Jordan M. Fletcher et al.   ACS Synthetic Biology

Dioxygen Activation in Soluble Methane Monooxygenase

(2011) Christine E. Tinberg et al.   ACCOUNTS OF CHEMICAL RESEARCH

Theoretical and Computational Protein Design

(2011) Ilan Samish et al.   Annual Review of Physical Chemistry

Rigid substructure search

(2011) D. Shirvanyants et al.   BIOINFORMATICS

Novel proteins: from fold to function

(2011) Betsy A Smith et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Hydrolytic catalysis and structural stabilization in a designed metalloprotein

(2011) Melissa L. Zastrow et al.   Nature Chemistry

Computational Design of Virus-Like Protein Assemblies on Carbon Nanotube Surfaces

(2011) G. Grigoryan et al.   SCIENCE

Computation-Guided Backbone Grafting of a Discontinuous Motif onto a Protein Scaffold

(2011) M. L. Azoitei et al.   SCIENCE

The LabelHash algorithm for substructure matching

(2010) Mark Moll et al.   BMC BIOINFORMATICS

Spectroscopic and metal-binding properties of DF3: an artificial protein able to accommodate different metal ions

(2010) Rafael Torres Martin de Rosales et al.   JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY

Probing Designability via a Generalized Model of Helical Bundle Geometry

(2010) Gevorg Grigoryan et al.   JOURNAL OF MOLECULAR BIOLOGY

Creation of a Type 1 Blue Copper Site within a de Novo Coiled-Coil Protein Scaffold

(2010) Daigo Shiga et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

CDD: a Conserved Domain Database for the functional annotation of proteins

(2010) A. Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

De novo design of a non-natural fold for an iron–sulfur protein: Alpha-helical coiled-coil with a four-iron four-sulfur cluster binding site in its central core

(2009) Joanna Grzyb et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

Computational protein design: Advances in the design and redesign of biomolecular nanostructures

(2009) Jeffery G. Saven   CURRENT OPINION IN COLLOID & INTERFACE SCIENCE

Cu(I) binding properties of a designed metalloprotein

(2009) Fei Xie et al.   JOURNAL OF INORGANIC BIOCHEMISTRY

Rational design of a structural and functional nitric oxide reductase

(2009) Natasha Yeung et al.   NATURE

Design and engineering of an O2 transport protein

(2009) Ronald L. Koder et al.   NATURE

Design of functional metalloproteins

(2009) Yi Lu et al.   NATURE

An artificial di-iron oxo-protein with phenol oxidase activity

(2009) Marina Faiella et al.   Nature Chemical Biology

Designing artificial enzymes by intuition and computation

(2009) Vikas Nanda et al.   Nature Chemistry

Nature of the protein universe

(2009) M. Levitt   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

De novo backbone scaffolds for protein design

(2009) James T. MacDonald et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Oxygen Reactivity of the Biferrous Site in the de novo Designed Four Helix Bundle Peptide DFsc: Nature of the “Intermediate” and Reaction Mechanism

(2008) Jennifer R. Calhoun et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

In vitro reconstitution and crystal structure of p-aminobenzoate N-oxygenase (AurF) involved in aureothin biosynthesis

(2008) Y. S. Choi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Computer-Based Redesign of a β Sandwich Protein Suggests that Extensive Negative Design Is Not Required for De Novo β Sheet Design

(2008) Xiaozhen Hu et al.   STRUCTURE

A de novo redesign of the WW domain

(2003) Christina M. Kraemer-Pecore et al.   PROTEIN SCIENCE

Thoroughly sampling sequence space: Large-scale protein design of structural ensembles

(2002) Stefan M. Larson et al.   PROTEIN SCIENCE