Mega-scale experimental analysis of protein folding stability in biology and design

Predicting and interpreting large-scale mutagenesis data using analyses of protein stability and conservation

(2022) Magnus Haraldson Høie et al.   Cell Reports

Dissecting the stability determinants of a challenging de novo protein fold using massively parallel design and experimentation

(2022) Tae-Eun Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Protein sequence design by conformational landscape optimization

(2021) Christoffer Norn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Community-Wide Experimental Evaluation of the PROSS Stability-Design Method

(2021) Yoav Peleg et al.   JOURNAL OF MOLECULAR BIOLOGY

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

Artificial intelligence challenges for predicting the impact of mutations on protein stability

(2021) Fabrizio Pucci et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

De novo protein design by deep network hallucination

(2021) Ivan Anishchenko et al.   NATURE

Improved protein structure prediction using predicted interresidue orientations

(2020) Jianyi Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A single mutation increases heavy chain heterodimer assembly of bispecific antibodies by inducing structural disorder in one homodimer species

(2020) Cian Stutz et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

DropSynth 2.0: high-fidelity multiplexed gene synthesis in emulsions

(2020) Angus M Sidore et al.   NUCLEIC ACIDS RESEARCH

Computational Modeling of Protein Stability: Quantitative Analysis Reveals Solutions to Pervasive Problems

(2020) Aron Broom et al.   STRUCTURE

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

(2020) Benjamin Basanta et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2020) Rahul Nikam et al.   NUCLEIC ACIDS RESEARCH

Biophysical and Mechanistic Models for Disease-Causing Protein Variants

(2019) Amelie Stein et al.   TRENDS IN BIOCHEMICAL SCIENCES

Global analysis of methionine oxidation provides a census of folding stabilities for the human proteome

(2019) Ethan J. Walker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Protein stability engineering insights revealed by domain-wide comprehensive mutagenesis

(2019) Alex Nisthal et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

GEMME: A Simple and Fast Global Epistatic Model Predicting Mutational Effects

(2019) Elodie Laine et al.   MOLECULAR BIOLOGY AND EVOLUTION

Unified rational protein engineering with sequence-based deep representation learning

(2019) Ethan C. Alley et al.   NATURE METHODS

Multiplexed gene synthesis in emulsions for exploring protein functional landscapes

(2018) Calin Plesa et al.   SCIENCE

De novo design of a fluorescence-activating β-barrel

(2018) Jiayi Dou et al.   NATURE

Deep generative models of genetic variation capture the effects of mutations

(2018) Adam J. Riesselman et al.   NATURE METHODS

Protein evolution speed depends on its stability and abundance and on chaperone concentrations

(2018) Luca Agozzino et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The EVcouplings Python framework for coevolutionary sequence analysis

(2018) Thomas A Hopf et al.   BIOINFORMATICS

Staphylococcus aureus Cas9 is a multiple-turnover enzyme

(2018) Paul Yourik et al.   RNA

Sequence statistics of tertiary structural motifs reflect protein stability

(2017) Fan Zheng et al.   PLoS One

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

(2017) Gabriel J. Rocklin et al.   SCIENCE

Automated Structure- and Sequence-Based Design of Proteins for High Bacterial Expression and Stability

(2016) Adi Goldenzweig et al.   MOLECULAR CELL

Structural basis of nucleic acid recognition by FK506-binding protein 25 (FKBP25), a nuclear immunophilin

(2016) Ajit Prakash et al.   NUCLEIC ACIDS RESEARCH

MAESTRO - multi agent stability prediction upon point mutations

(2015) Josef Laimer et al.   BMC BIOINFORMATICS

Protein folding of the SAP domain, a naturally occurring two-helix bundle

(2015) Charlotte A. Dodson et al.   FEBS LETTERS

Tertiary Structural Propensities Reveal Fundamental Sequence/Structure Relationships

(2015) Fan Zheng et al.   STRUCTURE

Quantitative proteomics reveals the kinetics of trypsin-catalyzed protein digestion

(2014) Yanbo Pan et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches

(2014) B. E. Suzek et al.   BIOINFORMATICS

Tracking cancer drugs in living cells by thermal profiling of the proteome

(2014) M. M. Savitski et al.   SCIENCE

PEAR: a fast and accurate Illumina Paired-End reAd mergeR

(2013) J. Zhang et al.   BIOINFORMATICS

Rational modification of protein stability by targeting surface sites leads to complicated results

(2013) S. Xiao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Stability-mediated epistasis constrains the evolution of an influenza protein

(2013) Lizhi Ian Gong et al.   eLife

A Single Mutation in Framework 2 of the Heavy Variable Domain Improves the Properties of a Diabody and a Related Single-Chain Antibody

(2012) Everardo Remi Rodríguez-Rodríguez et al.   JOURNAL OF MOLECULAR BIOLOGY

Principles for designing ideal protein structures

(2012) Nobuyasu Koga et al.   NATURE

A fundamental protein property, thermodynamic stability, revealed solely from large-scale measurements of protein function

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

RosettaRemodel: A Generalized Framework for Flexible Backbone Protein Design

(2011) Po-Ssu Huang et al.   PLoS One

Explaining complex codon usage patterns with selection for translational efficiency, mutation bias, and genetic drift

(2011) P. Shah et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Hidden Markov model speed heuristic and iterative HMM search procedure

(2010) L Steven Johnson et al.   BMC BIOINFORMATICS

A series of PDB related databases for everyday needs

(2010) R. P. Joosten et al.   NUCLEIC ACIDS RESEARCH

Analysis of Core Packing in a Cooperatively Folded Miniature Protein: The Ultrafast Folding Villin Headpiece Helical Subdomain

(2009) Shifeng Xiao et al.   BIOCHEMISTRY

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

Stability effects of mutations and protein evolvability

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

The Folding Mechanism of BBL: Plasticity of Transition-State Structure Observed within an Ultrafast Folding Protein Family

(2009) Hannes Neuweiler et al.   JOURNAL OF MOLECULAR BIOLOGY

cDNA display: a novel screening method for functional disulfide-rich peptides by solid-phase synthesis and stabilization of mRNA-protein fusions

(2009) J. Yamaguchi et al.   NUCLEIC ACIDS RESEARCH

Sequence determinants of thermodynamic stability in a WW domain-An all-β-sheet protein

(2009) Marcus Jäger et al.   PROTEIN SCIENCE

Increasing protein stability using a rational approach combining sequence homology and structural alignment: Stabilizing the WW domain

(2002) Xin Jiang et al.   PROTEIN SCIENCE