Dead-end elimination with perturbations (DEEPer): a provable protein design algorithm with continuous sidechain and backbone flexibility (Q30419532)

30 September 2017

Dead-end elimination with perturbations (DEEPer): a provable protein design algorithm with continuous sidechain and backbone flexibility (English)

1 reference

30 September 2017

0 references

1 reference

30 September 2017

Mark A Hallen

1 reference

30 September 2017

Bruce R Donald

series ordinal

1 reference

30 September 2017

language of work or name

English

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publication date

18 September 2012

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30 September 2017

1 reference

30 September 2017

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30 September 2017

1 reference

30 September 2017

18-39

1 reference

OSPREY: protein design with ensembles, flexibility, and provable algorithms

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3491125

The role of local backrub motions in evolved and designed mutations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3491125

Computational design of a PDZ domain peptide inhibitor that rescues CFTR activity

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3491125

Protein design using continuous rotamers

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3491125

Protein loop closure using orientational restraints from NMR data

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3491125

A new generation of crystallographic validation tools for the protein data bank

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3491125

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

20 June 2018

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3491125

20 June 2018

https://api.crossref.org/works/10.1002%2FPROT.24150

Computational design and experimental testing of the fastest-folding β-sheet protein

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3491125

Predicting resistance mutations using protein design algorithms

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3491125

KING (Kinemage, Next Generation): a versatile interactive molecular and scientific visualization program

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3491125

Computational structure-based redesign of enzyme activity

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3491125

The crystal structures of the psychrophilic subtilisin S41 and the mesophilic subtilisin Sph reveal the same calcium-loaded state

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3491125

Algorithm for backrub motions in protein design

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3491125

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3491125

Macromolecular modeling with rosetta

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3491125

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3491125

Matt: local flexibility aids protein multiple structure alignment.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3491125

Allosteric Inhibition of the Protein-Protein Interaction between the Leukemia-Associated Proteins Runx1 and CBFβ

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3491125

Dead-end elimination with backbone flexibility

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3491125

Progress in computational protein design

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3491125

Conformational entropy in molecular recognition by proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3491125

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3491125

Improved side-chain modeling for protein-protein docking

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3491125

The flexibility in the proline ring couples to the protein backbone

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3491125

Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chains

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3491125

Ab initio prediction of the three-dimensional structure of a de novo designed protein: a double-blind case study

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3491125

Conformational flexibility of PEP mutase

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3491125

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3491125

Rotation of the stalk/neck and one head in a new crystal structure of the kinesin motor protein, Ncd

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3491125

Structure validation by Calpha geometry: phi,psi and Cbeta deviation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3491125

Exact rotamer optimization for protein design

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3491125

Protein design is NP-hard

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3491125

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3491125

Native protein sequences are close to optimal for their structures

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3491125

The penultimate rotamer library

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3491125

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3491125

Effective energy function for proteins in solution

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3491125

Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3491125

High-resolution protein design with backbone freedom

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3491125

Direction determination in the minus-end-directed kinesin motor ncd

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3491125

Exploring the conformational space of protein side chains using dead-end elimination and the A* algorithm

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3491125

Standard conformations for the canonical structures of immunoglobulins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3491125

De novo design of the hydrophobic cores of proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3491125

Efficient rotamer elimination applied to protein side-chains and related spin glasses

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3491125

Monte Carlo-minimization approach to the multiple-minima problem in protein folding

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3491125

Structure of ubiquitin refined at 1.8 A resolution

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3491125

A mutant T4 lysozyme displays five different crystal conformations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3491125

Accurate prediction of the stability and activity effects of site-directed mutagenesis on a protein core

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3491125

Conformation of amino acid side-chains in proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3491125

A novel ensemble-based scoring and search algorithm for protein redesign and its application to modify the substrate specificity of the gramicidin synthetase a phenylalanine adenylation enzyme

20 June 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24150

Side-chain prediction by neural networks and simulated annealing optimization.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24150

Equation of State Calculations by Fast Computing Machines

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24150

A Formal Basis for the Heuristic Determination of Minimum Cost Paths

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24150

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24150

A kinematic view of loop closure

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24150

Molecular structure of proline.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24150

Improved Pruning algorithms and Divide-and-Conquer strategies for Dead-End Elimination, with application to protein design

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24150

Dead-end elimination for multistate protein design.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24150

AMBER: Assisted model building with energy refinement. A general program for modeling molecules and their interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24150

A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24150

An improved pairwise decomposable finite-difference Poisson-Boltzmann method for computational protein design

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24150

Fast and accurate algorithms for protein side-chain packing

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24150

Increased protein backbone conformational entropy upon hydrophobic ligand binding

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22821798

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1002/PROT.24150

1 reference

30 September 2017

1 reference

30 September 2017

PubMed publication ID

22821798

1 reference