Expanding the space of protein geometries by computational design of de novo fold families

What has de novo protein design taught us about protein folding and biophysics?

(2019) David Baker   PROTEIN SCIENCE

Computational design of structured loops for new protein functions

(2019) Kale Kundert et al.   BIOLOGICAL CHEMISTRY

Rapid Sampling of Hydrogen Bond Networks for Computational Protein Design

(2018) Jack B. Maguire et al.   Journal of Chemical Theory and Computation

De novo design of a fluorescence-activating β-barrel

(2018) Jiayi Dou et al.   NATURE

De novo design of a non-local β-sheet protein with high stability and accuracy

(2018) Enrique Marcos et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Rational design of proteins that exchange on functional timescales

(2017) James A Davey et al.   Nature Chemical Biology

COFACTOR: improved protein function prediction by combining structure, sequence and protein–protein interaction information

(2017) Chengxin Zhang et al.   NUCLEIC ACIDS RESEARCH

Principles for designing proteins with cavities formed by curved β sheets

(2017) Enrique Marcos et al.   SCIENCE

Global analysis of protein folding using massively parallel design, synthesis, and testing

(2017) Gabriel J. Rocklin et al.   SCIENCE

Simultaneous Optimization of Biomolecular Energy Functions on Features from Small Molecules and Macromolecules

(2016) Hahnbeom Park et al.   Journal of Chemical Theory and Computation

CATH: an expanded resource to predict protein function through structure and sequence

(2016) Natalie L. Dawson et al.   NUCLEIC ACIDS RESEARCH

Improving hybrid statistical and physical forcefields through local structure enumeration

(2016) Patrick Conway et al.   PROTEIN SCIENCE

Design of structurally distinct proteins using strategies inspired by evolution

(2016) T. M. Jacobs et al.   SCIENCE

Exploring the repeat protein universe through computational protein design

(2015) TJ Brunette et al.   NATURE

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

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

Control over overall shape and size in de novo designed proteins

(2015) Yu-Ru Lin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structure calculation, refinement and validation usingCcpNmr Analysis

(2015) Simon P. Skinner et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Rapid search for tertiary fragments reveals protein sequence-structure relationships

(2014) Jianfu Zhou et al.   PROTEIN SCIENCE

Computational design of water-soluble α-helical barrels

(2014) Andrew R. Thomson et al.   SCIENCE

High thermodynamic stability of parametrically designed helical bundles

(2014) Po-Ssu Huang et al.   SCIENCE

Ten years of probabilistic estimates of biocrystal solvent content: new insightsvianonparametric kernel density estimate

(2014) Christian X. Weichenberger et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

SCOPe: Structural Classification of Proteins—extended, integrating SCOP and ASTRAL data and classification of new structures

(2013) Naomi K. Fox et al.   NUCLEIC ACIDS RESEARCH

Towards automated crystallographic structure refinement withphenix.refine

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

An Amino Acid Packing Code for α-Helical Structure and Protein Design

(2012) Hyun Joo et al.   JOURNAL OF MOLECULAR BIOLOGY

Principles for designing ideal protein structures

(2012) Nobuyasu Koga et al.   NATURE

Generalized Fragment Picking in Rosetta: Design, Protocols and Applications

(2011) Dominik Gront et al.   PLoS One

A Smoothed Backbone-Dependent Rotamer Library for Proteins Derived from Adaptive Kernel Density Estimates and Regressions

(2011) Maxim V. Shapovalov et al.   STRUCTURE

XDS

(2010) Wolfgang Kabsch   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

PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta

(2010) S. Chaudhury et al.   BIOINFORMATICS

An exciting but challenging road ahead for computational enzyme design

(2010) David Baker   PROTEIN SCIENCE

RosettaHoles2: A volumetric packing measure for protein structure refinement and validation

(2010) William Sheffler et al.   PROTEIN SCIENCE

electronic Ligand Builder and Optimization Workbench(eLBOW): a tool for ligand coordinate and restraint generation

(2009) Nigel W. Moriarty et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

xia2: an expert system for macromolecular crystallography data reduction

(2009) G. Winter   JOURNAL OF APPLIED CRYSTALLOGRAPHY

DANGLE: A Bayesian inferential method for predicting protein backbone dihedral angles and secondary structure

(2009) Ming-Sin Cheung et al.   JOURNAL OF MAGNETIC RESONANCE

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