An enumerative algorithm for de novo design of proteins with diverse pocket structures

Macromolecular modeling and design in Rosetta: recent methods and frameworks

(2020) Julia Koehler Leman et al.   NATURE METHODS

Designing protein structures and complexes with the molecular modeling program Rosetta

(2019) Brian Kuhlman   JOURNAL OF BIOLOGICAL CHEMISTRY

Essentials of de novo protein design: Methods and applications

(2018) Enrique Marcos et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

De novo design of a fluorescence-activating β-barrel

(2018) Jiayi Dou et al.   NATURE

Design of metalloproteins and novel protein folds using variational autoencoders

(2018) Joe G. Greener et al.   Scientific Reports

Massively parallel de novo protein design for targeted therapeutics

(2017) Aaron Chevalier et al.   NATURE

Sampling and energy evaluation challenges in ligand binding protein design

(2017) Jiayi Dou et al.   PROTEIN SCIENCE

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

The coming of age of de novo protein design

(2016) Po-Ssu Huang et al.   NATURE

Design of structurally distinct proteins using strategies inspired by evolution

(2016) T. M. Jacobs et al.   SCIENCE

De novo protein design: how do we expand into the universe of possible protein structures?

(2015) Derek N Woolfson et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Exploring the repeat protein universe through computational protein design

(2015) TJ Brunette et al.   NATURE

Multiplex pairwise assembly of array-derived DNA oligonucleotides

(2015) Jason C. Klein et al.   NUCLEIC ACIDS RESEARCH

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

An amino acid code to define a protein's tertiary packing surface

(2015) Keith J. Fraga et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The origin of β-strand bending in globular proteins

(2015) Kazuo Fujiwara et al.   BMC STRUCTURAL BIOLOGY

Active Site Plasticity of a Computationally Designed Retro-Aldolase Enzyme

(2014) Richard Obexer et al.   ChemCatChem

Filling out the structural map of the NTF2-like superfamily

(2013) Ruth Y Eberhardt et al.   BMC BIOINFORMATICS

Computational design of ligand-binding proteins with high affinity and selectivity

(2013) Christine E. Tinberg et al.   NATURE

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

Computational Design of Catalytic Dyads and Oxyanion Holes for Ester Hydrolysis

(2012) Florian Richter et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Principles for designing ideal protein structures

(2012) Nobuyasu Koga et al.   NATURE

De Novo Enzyme Design Using Rosetta3

(2011) Florian Richter et al.   PLoS One

RosettaRemodel: A Generalized Framework for Flexible Backbone Protein Design

(2011) Po-Ssu Huang et al.   PLoS One

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

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

NWChem: A comprehensive and scalable open-source solution for large scale molecular simulations

(2010) M. Valiev et al.   COMPUTER PHYSICS COMMUNICATIONS

A practical generative design method

(2010) Sivam Krish   COMPUTER-AIDED DESIGN

Protein Pockets: Inventory, Shape, and Comparison

(2010) Ryan G. Coleman et al.   Journal of Chemical Information and Modeling

Probing Designability via a Generalized Model of Helical Bundle Geometry

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

Protein structure prediction: when is it useful?

(2009) Yang Zhang   CURRENT OPINION IN STRUCTURAL BIOLOGY