The Stability Landscape of de novo TIM Barrels Explored by a Modular Design Approach

Evolution, folding, and design of TIM barrels and related proteins

(2021) Sergio Romero-Romero et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

ProThermDB: thermodynamic database for proteins and mutants revisited after 15 years

(2020) Rahul Nikam et al.   NUCLEIC ACIDS RESEARCH

Tight and specific lanthanide binding in a de novo TIM barrel with a large internal cavity designed by symmetric domain fusion

(2020) Shane J. Caldwell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Networks of electrostatic and hydrophobic interactions modulate the complex folding free energy surface of a designed βα protein

(2019) Sujit Basak et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hydrophobic surface residues can stabilize a protein through improved water‐protein interactions

(2019) Mohammad M. Islam et al.   FEBS Journal

Double-mutant cycles: new directions and applications

(2019) Amnon Horovitz et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Principles of Protein Stability and Their Application in Computational Design

(2018) Adi Goldenzweig et al.   Annual Review of Biochemistry

MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update)

(2018) Lukáš Pravda et al.   NUCLEIC ACIDS RESEARCH

DIALS: implementation and evaluation of a new integration package

(2018) Graeme Winter et al.   Acta Crystallographica Section D-Structural Biology

The coming of age of de novo protein design

(2016) Po-Ssu Huang et al.   NATURE

Boosting protein stability with the computational design of β-sheet surfaces

(2016) Doo Nam Kim et al.   PROTEIN SCIENCE

Epistasis in protein evolution

(2016) Tyler N. Starr et al.   PROTEIN SCIENCE

How mutational epistasis impairs predictability in protein evolution and design

(2016) Charlotte M. Miton et al.   PROTEIN SCIENCE

XDSAPP2.0

(2016) Karine M. Sparta et al.   JOURNAL OF APPLIED CRYSTALLOGRAPHY

Design of symmetric TIM barrel proteins from first principles

(2015) Deepesh Nagarajan et al.   BMC BIOCHEMISTRY

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

(2015) Po-Ssu Huang et al.   Nature Chemical 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

Mutational Studies on Resurrected Ancestral Proteins Reveal Conservation of Site-Specific Amino Acid Preferences throughout Evolutionary History

(2014) Valeria A. Risso et al.   MOLECULAR BIOLOGY AND EVOLUTION

High thermodynamic stability of parametrically designed helical bundles

(2014) Po-Ssu Huang et al.   SCIENCE

Thermodynamic System Drift in Protein Evolution

(2014) Kathryn M. Hart et al.   PLOS BIOLOGY

ThePDB_REDOserver for macromolecular structure model optimization

(2014) Robbie P. Joosten et al.   IUCrJ

D3, the new diffractometer for the macromolecular crystallography beamlines of the Swiss Light Source

(2014) Martin R. Fuchs et al.   JOURNAL OF SYNCHROTRON RADIATION

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2013) Maximiliano Figueroa et al.   PLoS One

Mutational effects on stability are largely conserved during protein evolution

(2013) O. Ashenberg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Epistasis Among Adaptive Mutations in Deer Mouse Hemoglobin

(2013) C. Natarajan et al.   SCIENCE

Understanding Thermal Adaptation of Enzymes through the Multistate Rational Design and Stability Prediction of 100 Adenylate Kinases

(2013) Stanley C. Howell et al.   STRUCTURE

Folding the proteome

(2013) Esther Braselmann et al.   TRENDS IN BIOCHEMICAL SCIENCES

Temperature adaptations in psychrophilic, mesophilic and thermophilic chloride-dependent alpha-amylases

(2012) Alexandre Cipolla et al.   BIOCHIMIE

Principles for designing ideal protein structures

(2012) Nobuyasu Koga et al.   NATURE

Automated selection of stabilizing mutations in designed and natural proteins

(2012) B. Borgo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

SLS Crystallization Platform at Beamline X06DA—A Fully Automated Pipeline Enablingin SituX-ray Diffraction Screening

(2011) R. Bingel-Erlenmeyer et al.   CRYSTAL GROWTH & DESIGN

Regulatory evolution through divergence of a phosphoswitch in the transcription factor CEBPB

(2011) Vincent J. Lynch et al.   NATURE

XDS

(2010) Wolfgang Kabsch   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Features and development ofCoot

(2010) P. Emsley et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

PHENIX: a comprehensive Python-based system for macromolecular structure solution

(2010) Paul D. Adams et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

MolProbity: all-atom structure validation for macromolecular crystallography

(2009) Vincent B. Chen et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

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

(2009) Birte Höcker et al.   BIOCHEMISTRY

Stability effects of mutations and protein evolvability

(2009) Nobuhiko Tokuriki et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Between-Species Variation in the Kinetic Stability of TIM Proteins Linked to Solvation-Barrier Free Energies

(2008) Miguel Costas et al.   JOURNAL OF MOLECULAR BIOLOGY