A generic program for multistate protein design (Q33960287)

30 July 2017

A generic program for multistate protein design (English)

1 reference

30 July 2017

0 references

4

Brian Kuhlman

1 reference

30 July 2017

1

Andrew Leaver-Fay

1 reference

30 July 2017

Ron Jacak

2

1 reference

PubMed ID

21754981

30 July 2017

P Benjamin Stranges

series ordinal

3

1 reference

PubMed ID

21754981

30 July 2017

language of work or name

English

0 references

publication date

6 July 2011

1 reference

30 July 2017

1 reference

30 July 2017

6

1 reference

30 July 2017

7

1 reference

30 July 2017

e20937

1 reference

Creative Commons Attribution 4.0 International

30 July 2017

start time

6 July 2011

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

RosettaScripts: a scripting language interface to the Rosetta macromolecular modeling suite

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3130737

Computational Design of Proteins Targeting the Conserved Stem Region of Influenza Hemagglutinin

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3130737

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

5 July 2018

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3130737

5 July 2018

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0020937

ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3130737

RalBP1 is necessary for metastasis of human cancer cell lines

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3130737

Generation of longer emission wavelength red fluorescent proteins using computationally designed libraries

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3130737

Computational design of orthogonal nucleoside kinases

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3130737

The RalB-RLIP76 Complex Reveals a Novel Mode of Ral-Effector Interaction

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3130737

Computational Design of an Enzyme Catalyst for a Stereoselective Bimolecular Diels-Alder Reaction

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3130737

Computational reprogramming of homing endonuclease specificity at multiple adjacent base pairs

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3130737

Tradeoff between stability and multispecificity in the design of promiscuous proteins

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3130737

Computer-aided design of functional protein interactions

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3130737

Computational design of affinity and specificity at protein-protein interfaces

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3130737

Design of protein-interaction specificity gives selective bZIP-binding peptides.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3130737

Kemp elimination catalysts by computational enzyme design

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3130737

De novo computational design of retro-aldol enzymes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3130737

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3130737

Ral GTPases and cancer: linchpin support of the tumorigenic platform

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3130737

Design of multi-specificity in protein interfaces

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3130737

Progress in computational protein design

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3130737

Full-sequence computational design and solution structure of a thermostable protein variant

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3130737

Emergence of protein fold families through rational design

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3130737

Ultra-fast evaluation of protein energies directly from sequence

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3130737

Dramatic performance enhancements for the FASTER optimization algorithm

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3130737

The new face of bispecific antibodies: targeting cancer and much more

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3130737

Activation of RalA is critical for Ras-induced tumorigenesis of human cells.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3130737

Exo84 and Sec5 are competitive regulatory Sec6/8 effectors to the RalA GTPase

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3130737

WebLogo: A Sequence Logo Generator

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3130737

Protein structure prediction using Rosetta

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3130737

Design of a Novel Globular Protein Fold with Atomic-Level Accuracy

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3130737

Ral GTPases regulate exocyst assembly through dual subunit interactions

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3130737

A large scale test of computational protein design: folding and stability of nine completely redesigned globular proteins

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3130737

Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3130737

Structural basis of the interaction between RalA and Sec5, a subunit of the sec6/8 complex

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3130737

Protein design is NP-hard

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3130737

Rotamer libraries in the 21st century

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3130737

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3130737

Accurate computer-based design of a new backbone conformation in the second turn of protein L

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3130737

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3130737

Native protein sequences are close to optimal for their structures

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3130737

Computational design of an integrin I domain stabilized in the open high affinity conformation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3130737

The penultimate rotamer library

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3130737

High-resolution protein design with backbone freedom

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3130737

Design, structure and stability of a hyperthermophilic protein variant

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3130737

De novo protein design: fully automated sequence selection

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3130737

Bayesian statistical analysis of protein side-chain rotamer preferences

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3130737

Identification and characterization of Ral-binding protein 1, a potential downstream target of Ral GTPases

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3130737

Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3130737

Rationally designed integrin beta3 mutants stabilized in the high affinity conformation

5 July 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0020937

Automated design of specificity in molecular recognition

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0020937

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0020937

Equation of State Calculations by Fast Computing Machines

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0020937

A designed heterotrimeric coiled coil

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0020937

Protein design simulations suggest that side-chain conformational entropy is not a strong determinant of amino acid environmental preferences

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0020937

Accounting for conformational entropy in predicting binding free energies of protein-protein interactions.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0020937

Design of multispecific protein sequences using probabilistic graphical modeling.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3130737

An efficient algorithm for multistate protein design based on FASTER.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3130737

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

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3130737

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

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3130737

10.1371/JOURNAL.PONE.0020937

29 October 2018

Identifiers

DOI

1 reference

30 July 2017

0 references

1 reference

30 July 2017

1 reference

PubMed ID

21754981