4.8 Article

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

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Multidisciplinary Sciences

Cell-wide analysis of protein thermal unfolding reveals determinants of thermostability

Pascal Leuenberger et al.

SCIENCE (2017)

Article Chemistry, Physical

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

Hahnbeom Park et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2016)

Article Multidisciplinary Sciences

Accurate de novo design of hyperstable constrained peptides

Gaurav Bhardwaj et al.

NATURE (2016)

Review Multidisciplinary Sciences

The coming of age of de novo protein design

Po-Ssu Huang et al.

NATURE (2016)

Article Biochemistry & Molecular Biology

The MPI bioinformatics Toolkit as an integrative platform for advanced protein sequence and structure analysis

Vikram Alva et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Multidisciplinary Sciences

Protein engineering by highly parallel screening of computationally designed variants

Mark G. F. Sun et al.

SCIENCE ADVANCES (2016)

Article Biochemistry & Molecular Biology

Protein stability: computation, sequence statistics, and new experimental methods

Thomas J. Magliery

CURRENT OPINION IN STRUCTURAL BIOLOGY (2015)

Article Chemistry, Multidisciplinary

Fluorescence Correlation Spectroscopy Reveals Highly Efficient Cytosolic Delivery of Certain Penta-Arg Proteins and Stapled Peptides

Jonathan R. LaRochelle et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2015)

Article Biochemistry & Molecular Biology

Local and macroscopic electrostatic interactions in single α-helices

Emily G. Baker et al.

NATURE CHEMICAL BIOLOGY (2015)

Article Multidisciplinary Sciences

Control over overall shape and size in de novo designed proteins

Yu-Ru Lin et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)

Article Biochemistry & Molecular Biology

Tertiary Structural Propensities Reveal Fundamental Sequence/Structure Relationships

Fan Zheng et al.

STRUCTURE (2015)

Article Biochemical Research Methods

Quantitative proteomics reveals the kinetics of trypsin-catalyzed protein digestion

Yanbo Pan et al.

ANALYTICAL AND BIOANALYTICAL CHEMISTRY (2014)

Article Biochemical Research Methods

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

Jiajie Zhang et al.

BIOINFORMATICS (2014)

Article Biochemistry & Molecular Biology

Assessing the accuracy of physical models used in protein-folding simulations: quantitative evidence from long molecular dynamics simulations

Stefano Piana et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2014)

Review Biochemistry & Molecular Biology

Forces stabilizing proteins

C. Nick Pace et al.

FEBS LETTERS (2014)

Article Chemistry, Multidisciplinary

Folding Simulations for Proteins with Diverse Topologies Are Accessible in Days with a Physics-Based Force Field and Implicit Solvent

Hai Nguyen et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2014)

Review Biochemical Research Methods

Large-scale de novo DNA synthesis: technologies and applications

Sriram Kosuri et al.

NATURE METHODS (2014)

Article Biochemistry & Molecular Biology

Contribution of hydrogen bonds to protein stability

C. Nick Pace et al.

PROTEIN SCIENCE (2014)

Review Biophysics

Fast protein folding kinetics

Hannah Gelman et al.

QUARTERLY REVIEWS OF BIOPHYSICS (2014)

Review Biophysics

Energy Functions in De Novo Protein Design: Current Challenges and Future Prospects

Zhixiu Li et al.

ANNUAL REVIEW OF BIOPHYSICS, VOL 42 (2013)

Article Multidisciplinary Sciences

Navigating the protein fitness landscape with Gaussian processes

Philip A. Romero et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)

Article Multidisciplinary Sciences

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

Shifeng Xiao et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)

Article Biochemistry & Molecular Biology

Arginine Topology Controls Escape of Minimally Cationic Proteins from Early Endosomes to the Cytoplasm

Jacob S. Appelbaum et al.

CHEMISTRY & BIOLOGY (2012)

Article Multidisciplinary Sciences

Principles for designing ideal protein structures

Nobuyasu Koga et al.

NATURE (2012)

Article Biochemical Research Methods

HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment

Michael Remmert et al.

NATURE METHODS (2012)

Article Multidisciplinary Sciences

Protein folding kinetics and thermodynamics from atomistic simulation

Stefano Piana et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)

Article Multidisciplinary Sciences

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

Carlos L. Araya et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)

Article Chemistry, Multidisciplinary

Accelerated NMR Spectroscopy by Using Compressed Sensing

Krzysztof Kazimierczuk et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2011)

Article Biochemistry & Molecular Biology

A novel strategy for NMR resonance assignment and protein structure determination

Alexander Lemak et al.

JOURNAL OF BIOMOLECULAR NMR (2011)

Article Biochemistry & Molecular Biology

Contribution of Hydrophobic Interactions to Protein Stability

C. Nick Pace et al.

JOURNAL OF MOLECULAR BIOLOGY (2011)

Article Multidisciplinary Sciences

RosettaRemodel: A Generalized Framework for Flexible Backbone Protein Design

Po-Ssu Huang et al.

PLOS ONE (2011)

Article Multidisciplinary Sciences

How Fast-Folding Proteins Fold

Kresten Lindorff-Larsen et al.

SCIENCE (2011)

Article Computer Science, Interdisciplinary Applications

Learning Bayesian Networks with the bnlearn R Package

Marco Scutari

JOURNAL OF STATISTICAL SOFTWARE (2010)

Article Biochemistry & Molecular Biology

An improved yeast transformation method for the generation of very large human antibody libraries

Lorenzo Benatuil et al.

PROTEIN ENGINEERING DESIGN & SELECTION (2010)

Article Chemistry, Multidisciplinary

De Novo Design of a beta alpha beta Motif

Huanhuan Liang et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2009)

Article Biochemistry & Molecular Biology

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

Hannes Neuweiler et al.

JOURNAL OF MOLECULAR BIOLOGY (2009)

Article Biochemical Research Methods

Enzymatic assembly of DNA molecules up to several hundred kilobases

Daniel G. Gibson et al.

NATURE METHODS (2009)

Article Biochemistry & Molecular Biology

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

Marcus Jaeger et al.

PROTEIN SCIENCE (2009)

Article Biochemistry & Molecular Biology

Sequence specific resonance assignment via Multicanonical Monte Carlo search using an ABACUS approach

Alexander Lemak et al.

JOURNAL OF BIOMOLECULAR NMR (2008)

Article Biochemistry & Molecular Biology

Energetics-based protein profiling on a proteomic scale: Identification of proteins resistant to proteolysis

Chiwook Park et al.

JOURNAL OF MOLECULAR BIOLOGY (2007)

Article Biotechnology & Applied Microbiology

Improving catalytic function by ProSAR-driven enzyme evolution

Richard J. Fox et al.

NATURE BIOTECHNOLOGY (2007)

Article Biochemistry & Molecular Biology

Evaluating protein structures determined by structural genomics consortia

Aneerban Bhattacharya et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2007)

Article Multidisciplinary Sciences

Structure-function-folding relationship in a WW domain

Marcus Jaeger et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)

Article Biochemistry & Molecular Biology

An expanded WW domain recognition motif revealed by the interaction between Smad7 and the E3 ubiquitin ligase Smurf2

P. Andrew Chong et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2006)

Article Biochemical Research Methods

Isolating and engineering human antibodies using yeast surface display

Ginger Chao et al.

NATURE PROTOCOLS (2006)

Article Biochemistry & Molecular Biology

ProTherm and ProNIT: thermodynamic databases for proteins and protein-nucleic acid interactions

M. D. Shaji Kumar et al.

NUCLEIC ACIDS RESEARCH (2006)

Article Biotechnology & Applied Microbiology

Yeast surface display of a noncovalent MHC class II heterodimer complexed with antigenic peptide

ET Boder et al.

BIOTECHNOLOGY AND BIOENGINEERING (2005)

Article Biochemical Research Methods

Protein production by auto-induction in high-density shaking cultures

FW Studier

PROTEIN EXPRESSION AND PURIFICATION (2005)

Review Biochemistry & Molecular Biology

De novo proteins from designed combinatorial libraries

MH Hecht et al.

PROTEIN SCIENCE (2004)

Article Biochemistry & Molecular Biology

WebLogo: A sequence logo generator

GE Crooks et al.

GENOME RESEARCH (2004)

Article Biochemistry & Molecular Biology

Optimizing resolution in multidimensional NMR by three-way decomposition

VY Orekhov et al.

JOURNAL OF BIOMOLECULAR NMR (2003)

Article Biochemistry & Molecular Biology

Refinement of protein structures in explicit solvent

JP Linge et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2003)

Article Biochemistry & Molecular Biology

DNAWorks: an automated method for designing oligonucleotides for PCR-based gene synthesis

DM Hoover et al.

NUCLEIC ACIDS RESEARCH (2002)

Article Biochemistry & Molecular Biology

Prediction of functionally important residues based solely on the computed energetics of protein structure

AH Elcock

JOURNAL OF MOLECULAR BIOLOGY (2001)

Article Biochemistry & Molecular Biology

Structural basis for phosphoserine-proline recognition by group IVWW domains

MA Verdecia et al.

NATURE STRUCTURAL BIOLOGY (2000)