Combinatorial methods for small-molecule placement in computational enzyme design (Q33262158)

24 July 2017

title

Combinatorial methods for small-molecule placement in computational enzyme design (English)

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24 July 2017

author name string

Jonathan Kyle Lassila

1

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24 July 2017

Heidi K Privett

2

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24 July 2017

Benjamin D Allen

3

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24 July 2017

Stephen L Mayo

4

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24 July 2017

language of work or name

English

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publication date

30 October 2006

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Proceedings of the National Academy of Sciences of the United States of America

24 July 2017

number of pages

6

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based on heuristic

inferred from page(s)

published in

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24 July 2017

volume

103

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24 July 2017

issue

45

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24 July 2017

page(s)

16710-16715

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Dramatic performance enhancements for the FASTER optimization algorithm

24 July 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1636520

Cooperative hydrogen bond interactions in the streptavidin-biotin system

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1636520

Electrostatics in computational protein design

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1636520

Sequence optimization and designability of enzyme active sites

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1636520

Advantages of fine-grained side chain conformer libraries

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1636520

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1636520

A perspective on enzyme catalysis.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1636520

Computational design of receptor and sensor proteins with novel functions

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1636520

Challenges in enzyme mechanism and energetics

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1636520

Optimal alignment for enzymatic proton transfer: structure of the Michaelis complex of triosephosphate isomerase at 1.2-A resolution.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1636520

Exact rotamer optimization for protein design

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1636520

Protein design is NP-hard

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1636520

A review of protein-small molecule docking methods

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1636520

Energy estimation in protein design

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1636520

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1636520

Enzyme-like proteins by computational design

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1636520

Extending the accuracy limits of prediction for side-chain conformations

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1636520

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1636520

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1636520

Effective energy function for proteins in solution

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1636520

Design, structure and stability of a hyperthermophilic protein variant

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1636520

De novo protein design: fully automated sequence selection

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1636520

Probing the role of packing specificity in protein design

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1636520

Bayesian statistical analysis of protein side-chain rotamer preferences

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1636520

Automated design of the surface positions of protein helices

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1636520

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1636520

Construction of new ligand binding sites in proteins of known structure

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1636520

Computational design of a biologically active enzyme

28 July 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0607691103

Computational prediction of native protein ligand-binding and enzyme active site sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0607691103

Pairwise calculation of protein solvent-accessible surface areas

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0607691103

Computationally designed variants of Escherichia coli chorismate mutase show altered catalytic activity

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0607691103

De novo design of biocatalysts

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0607691103

Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0607691103

Equation of State Calculations by Fast Computing Machines

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0607691103

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

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1636520

The penultimate rotamer library

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1636520

31 October 2018

Identifiers

DOI

10.1073/PNAS.0607691103

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24 July 2017

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24 July 2017

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