New algorithms and an in silico benchmark for computational enzyme design (Q42036773)

15 October 2017

New algorithms and an in silico benchmark for computational enzyme design (English)

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15 October 2017

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5

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15 October 2017

Daniela Röthlisberger

7

object named as

Daniela Röthlisberger

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David Baker

object named as

David Baker

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author name string

Alexandre Zanghellini

1

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15 October 2017

Lin Jiang

2

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15 October 2017

Andrew M Wollacott

3

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15 October 2017

Gong Cheng

4

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15 October 2017

Eric A Althoff

6

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15 October 2017

Daniela Röthlisberger

7

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15 October 2017

1 December 2006

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15 October 2017

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15 October 2017

15

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15 October 2017

12

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15 October 2017

2785-2794

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Improved side-chain modeling for protein-protein docking

15 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242439

A "solvated rotamer" approach to modeling water-mediated hydrogen bonds at protein-protein interfaces

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242439

De novo design of catalytic proteins

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242439

Exploring folding free energy landscapes using computational protein design.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242439

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242439

Protein-protein docking predictions for the CAPRI experiment

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242439

A simple physical model for binding energy hot spots in protein-protein complexes

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242439

5 June 2018

The Protein Data Bank

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242439

Enzyme-like proteins by computational design

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242439

Native protein sequences are close to optimal for their structures

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242439

Critical analysis of antibody catalysis.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242439

Effective energy function for proteins in solution

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242439

Theozymes and compuzymes: theoretical models for biological catalysis

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242439

Detection of protein three-dimensional side-chain patterns: new examples of convergent evolution.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242439

De novo protein design: fully automated sequence selection

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242439

Bayesian statistical analysis of protein side-chain rotamer preferences

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242439

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242439

Protein design automation

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242439

A computer vision based technique for 3-D sequence-independent structural comparison of proteins

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242439

At the crossroads of chemistry and immunology: catalytic antibodies

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242439

Construction of new ligand binding sites in proteins of known structure

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242439

ROSETTALIGAND: protein-small molecule docking with full side-chain flexibility.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242439

Computational design of a biologically active enzyme

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242439

Computational redesign of protein-protein interaction specificity

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242439

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

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242439

Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins

17 August 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17132862

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Metal search: a computer program that helps design tetrahedral metal-binding sites

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17132862

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1110/PS.062353106

1 reference

15 October 2017

1 reference

15 October 2017

PubMed publication ID

17132862

1 reference