Computer-aided design of functional protein interactions (Q37617943)

21 August 2017

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title

Computer-aided design of functional protein interactions (English)

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21 August 2017

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computer-aided design

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2

Tanja Kortemme

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21 August 2017

Daniel J Mandell

1

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21 August 2017

1 November 2009

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21 August 2017

Nature Chemical Biology

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21 August 2017

5

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21 August 2017

797-807

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21 August 2017

11

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https://scigraph.springernature.com/pub.10.1038/nchembio.251

21 August 2017

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Computer-aided design of a PDZ domain to recognize new target sequences.

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Modulating calmodulin binding specificity through computational protein design

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Ca2+ indicators based on computationally redesigned calmodulin-peptide pairs

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Computational design of receptor and sensor proteins with novel functions

21 January 2018

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Computational redesign of endonuclease DNA binding and cleavage specificity

21 January 2018

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De novo computational design of retro-aldol enzymes

21 January 2018

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Kemp elimination catalysts by computational enzyme design

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Effective energy function for proteins in solution

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Computer-based design of novel protein structures

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Potential energy functions for protein design.

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Electrostatics in computational protein design

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Structure-based Protocol for Identifying Mutations that Enhance Protein–Protein Binding Affinities

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Rational design of intercellular adhesion molecule-1 (ICAM-1) variants for antagonizing integrin lymphocyte function-associated antigen-1-dependent adhesion

21 January 2018

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Computational Redesign of the SHV-1 β-Lactamase/β-Lactamase Inhibitor Protein Interface

21 January 2018

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Identification and rational redesign of peptide ligands to CRIP1, a novel biomarker for cancers

21 January 2018

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Computational design of a new hydrogen bond network and at least a 300-fold specificity switch at a protein-protein interface.

21 January 2018

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Automated design of specificity in molecular recognition

21 January 2018

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Specificity versus stability in computational protein design

21 January 2018

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A chemical switch for inhibitor-sensitive alleles of any protein kinase

21 January 2018

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Evidence for dynamically organized modularity in the yeast protein-protein interaction network

21 January 2018

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Design of multi-specificity in protein interfaces

21 January 2018

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A de novo designed protein protein interface

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Phage display for engineering and analyzing protein interaction interfaces

21 January 2018

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Large-scale prediction of protein geometry and stability changes for arbitrary single point mutations

21 January 2018

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Comprehensive and quantitative mapping of energy landscapes for protein-protein interactions by rapid combinatorial scanning

21 January 2018

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A specificity map for the PDZ domain family

21 January 2018

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Design of protein conformational switches

21 January 2018

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Modeling backbone flexibility to achieve sequence diversity: the design of novel alpha-helical ligands for Bcl-xL.

21 January 2018

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Thoroughly sampling sequence space: large-scale protein design of structural ensembles

21 January 2018

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Emergence of protein fold families through rational design

21 January 2018

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Prediction of protein-protein interface sequence diversity using flexible backbone computational protein design

21 January 2018

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A Correspondence Between Solution-State Dynamics of an Individual Protein and the Sequence and Conformational Diversity of its Family

21 January 2018

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Computational design of a single amino acid sequence that can switch between two distinct protein folds.

21 January 2018

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High-resolution design of a protein loop

21 January 2018

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Recapitulation of protein family divergence using flexible backbone protein design

21 January 2018

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Backrub-like backbone simulation recapitulates natural protein conformational variability and improves mutant side-chain prediction

21 January 2018

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Eris: an automated estimator of protein stability.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCHEMBIO.251

Dead-end elimination with backbone flexibility

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCHEMBIO.251

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCHEMBIO.251

A simple model of backbone flexibility improves modeling of side-chain conformational variability

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCHEMBIO.251

Computationally designed libraries of fluorescent proteins evaluated by preservation and diversity of function

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCHEMBIO.251

Nonnatural protein-protein interaction-pair design by key residues grafting

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCHEMBIO.251

Computational redesign of a protein-protein interface for high affinity and binding specificity using modular architecture and naturally occurring template fragments

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCHEMBIO.251

New algorithms and an in silico benchmark for computational enzyme design

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCHEMBIO.251

Motif-directed flexible backbone design of functional interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCHEMBIO.251

Alteration of enzyme specificity by computational loop remodeling and design

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCHEMBIO.251

Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCHEMBIO.251

Ultra-fast evaluation of protein energies directly from sequence

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCHEMBIO.251

Proteome survey reveals modularity of the yeast cell machinery

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCHEMBIO.251

Global landscape of protein complexes in the yeast Saccharomyces cerevisiae

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCHEMBIO.251

Exploration of the function and organization of the yeast early secretory pathway through an epistatic miniarray profile

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCHEMBIO.251

Side-chain repacking calculations for predicting structures and stabilities of heterodimeric coiled coils

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCHEMBIO.251

Computational design and experimental study of tighter binding peptides to an inactivated mutant of HIV-1 protease

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCHEMBIO.251

Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCHEMBIO.251

Modeling structurally variable regions in homologous proteins with rosetta.

21 January 2018

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https://api.crossref.org/works/10.1038%2FNCHEMBIO.251

Protein-protein docking with backbone flexibility.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCHEMBIO.251

Toward full-sequence de novo protein design with flexible templates for human beta-defensin-2.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCHEMBIO.251

The backrub motion: how protein backbone shrugs when a sidechain dances

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCHEMBIO.251

Algorithm for backrub motions in protein design

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCHEMBIO.251

Rotamer libraries in the 21st century

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCHEMBIO.251

Computer search algorithms in protein modification and design.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCHEMBIO.251

Native protein sequences are close to optimal for their structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCHEMBIO.251

Dramatic performance enhancements for the FASTER optimization algorithm

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCHEMBIO.251

Fast and accurate side-chain topology and energy refinement (FASTER) as a new method for protein structure optimization.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCHEMBIO.251

Trading accuracy for speed: A quantitative comparison of search algorithms in protein sequence design

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCHEMBIO.251

Energy functions for protein design

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCHEMBIO.251

An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCHEMBIO.251

Energy functions for protein design: adjustment with protein-protein complex affinities, models for the unfolded state, and negative design of solubility and specificity.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCHEMBIO.251

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCHEMBIO.251

The dead-end elimination theorem and its use in protein side-chain positioning

21 January 2018

2 references

https://api.crossref.org/works/10.1038%2FNCHEMBIO.251

21 January 2018

12 December 2020

Progress in modeling of protein structures and interactions

1 reference

12 December 2020

Ab initio protein structure prediction of CASP III targets using ROSETTA

1 reference

12 December 2020

Electrostatic design of protein-protein association rates

1 reference

12 December 2020

Backbone flexibility in computational protein design

1 reference

12 December 2020

An efficient algorithm for multistate protein design based on FASTER.

1 reference

12 December 2020

Identifiers

DOI

10.1038/NCHEMBIO.251

1 reference

21 August 2017

1 reference

PubMed ID

19841629