A general-purpose protein design framework based on mining sequence–structure relationships in known protein structures

Tertiary Structural Motif Sequence Statistics Enable Facile Prediction and Design of Peptides that Bind Anti-apoptotic Bfl-1 and Mcl-1

(2019) Vincent Frappier et al.   STRUCTURE

A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core

(2018) Lukas Zimmermann et al.   JOURNAL OF MOLECULAR BIOLOGY

De Novo Design of Tetranuclear Transition Metal Clusters Stabilized by Hydrogen-Bonded Networks in Helical Bundles

(2018) Shao-Qing Zhang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Accurate computational design of multipass transmembrane proteins

(2018) Peilong Lu et al.   SCIENCE

Computational Protein Design with Deep Learning Neural Networks

(2018) Jingxue Wang et al.   Scientific Reports

OSPREY 3.0: Open-source protein redesign for you, with powerful new features

(2018) Mark A. Hallen et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Sequence statistics of tertiary structural motifs reflect protein stability

(2017) Fan Zheng et al.   PLoS One

De novo design of covalently constrained mesosize protein scaffolds with unique tertiary structures

(2017) Bobo Dang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2017) Gabriel J. Rocklin et al.   SCIENCE

Computational protein design with backbone plasticity

(2016) James T. MacDonald et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

An Atomistic Statistically Effective Energy Function for Computational Protein Design

(2016) Christopher M. Topham et al.   Journal of Chemical Theory and Computation

Proteins of well-defined structures can be designed without backbone readjustment by a statistical model

(2016) Xiaoqun Zhou et al.   JOURNAL OF STRUCTURAL BIOLOGY

The coming of age of de novo protein design

(2016) Po-Ssu Huang et al.   NATURE

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

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

Tertiary alphabet for the observable protein structural universe

(2016) Craig O. Mackenzie et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Why reinvent the wheel? Building new proteins based on ready-made parts

(2016) Olga Khersonsky et al.   PROTEIN SCIENCE

Computational Design of Selective Peptides to Discriminate between Similar PDZ Domains in an Oncogenic Pathway

(2015) Fan Zheng et al.   JOURNAL OF MOLECULAR BIOLOGY

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

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

The I-TASSER Suite: protein structure and function prediction

(2015) Jianyi Yang et al.   NATURE METHODS

Tertiary Structural Propensities Reveal Fundamental Sequence/Structure Relationships

(2015) Fan Zheng et al.   STRUCTURE

Data-Driven Prediction and Design of bZIP Coiled-Coil Interactions

(2015) Vladimir Potapov et al.   PLoS Computational Biology

Automatic Prediction of Protein 3D Structures by Probabilistic Multi-template Homology Modeling

(2015) Armin Meier et al.   PLoS Computational Biology

Rapid search for tertiary fragments reveals protein sequence-structure relationships

(2014) Jianfu Zhou et al.   PROTEIN SCIENCE

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

(2014) Nathan H. Joh et al.   SCIENCE

Protein design with a comprehensive statistical energy function and boosted by experimental selection for foldability

(2014) Peng Xiong et al.   Nature Communications

Absolute free energies of biomolecules from unperturbed ensembles

(2013) Gevorg Grigoryan   JOURNAL OF COMPUTATIONAL CHEMISTRY

Computational protein design: The proteus software and selected applications

(2013) Thomas Simonson et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

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

(2013) Pralay Mitra et al.   NUCLEIC ACIDS RESEARCH

A Pareto-Optimal Refinement Method for Protein Design Scaffolds

(2013) Lucas Gregorio Nivón et al.   PLoS One

Relaxation of backbone bond geometry improves protein energy landscape modeling

(2013) Patrick Conway et al.   PROTEIN SCIENCE

An Evolution-Based Approach to De Novo Protein Design and Case Study on Mycobacterium tuberculosis

(2013) Pralay Mitra et al.   PLoS Computational Biology

Principles for designing ideal protein structures

(2012) Nobuyasu Koga et al.   NATURE

A highly stable protein chimera built from fragments of different folds

(2012) S. Shanmugaratnam et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Computational Design of a PDZ Domain Peptide Inhibitor that Rescues CFTR Activity

(2012) Kyle E. Roberts et al.   PLoS Computational Biology

A graphical interface for the FoldX forcefield

(2011) J. Van Durme et al.   BIOINFORMATICS

Protein design with fragment databases

(2011) Erik Verschueren et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

OPM database and PPM web server: resources for positioning of proteins in membranes

(2011) Mikhail A. Lomize et al.   NUCLEIC ACIDS RESEARCH

Algorithm discovery by protein folding game players

(2011) F. Khatib et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2011) Maxim V. Shapovalov et al.   STRUCTURE

Optimizing energy functions for protein-protein interface design

(2010) Oz Sharabi et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Alternate States of Proteins Revealed by Detailed Energy Landscape Mapping

(2010) Michael D. Tyka et al.   JOURNAL OF MOLECULAR BIOLOGY

Salt bridges: Geometrically specific, designable interactions

(2010) Jason E. Donald et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The fluorescent protein palette: tools for cellular imaging

(2009) Richard N. Day et al.   CHEMICAL SOCIETY REVIEWS

Backbone flexibility in computational protein design

(2009) Daniel J Mandell et al.   CURRENT OPINION IN BIOTECHNOLOGY

Computational structure-based redesign of enzyme activity

(2009) C.-Y. Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The minimized dead-end elimination criterion and its application to protein redesign in a hybrid scoring and search algorithm for computing partition functions over molecular ensembles

(2008) Ivelin Georgiev et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY