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Computational tools for designing and engineering enzymes

Current opinion in chemical biology, 2014-04, Vol.19, p.8-16

2014

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CAVER Analyst 2.0: analysis and visualization of channels and tunnels in protein structures and molecular dynamics trajectories

Bioinformatics, 2018-10, Vol.34 (20), p.3586-3588

2018

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PredictSNP: robust and accurate consensus classifier for prediction of disease-related mutations

PLoS computational biology, 2014-01, Vol.10 (1), p.e1003440

2014

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CAVER 3.0: a tool for the analysis of transport pathways in dynamic protein structures

PLoS computational biology, 2012-10, Vol.8 (10), p.e1002708

2012

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HotSpot Wizard 2.0: automated design of site-specific mutations and smart libraries in protein engineering

Nucleic acids research, 2016-07, Vol.44 (W1), p.W479

2016

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FireProt: Energy- and Evolution-Based Computational Design of Thermostable Multiple-Point Mutants

PLoS computational biology, 2015-11, Vol.11 (11), p.e1004556

2015

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Ancestral Haloalkane Dehalogenases Show Robustness and Unique Substrate Specificity

Chembiochem : a European journal of chemical biology, 2017-07, Vol.18 (14), p.1448-1456

2017

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Computational tools for designing and engineering biocatalysts

Current opinion in chemical biology, 2009-02, Vol.13 (1), p.26-34

2009

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CAVER: Algorithms for Analyzing Dynamics of Tunnels in Macromolecules

IEEE/ACM transactions on computational biology and bioinformatics, 2016-05, Vol.13 (3), p.505-517

2016

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CAVER Analyst 1.0: graphic tool for interactive visualization and analysis of tunnels and channels in protein structures

Bioinformatics (Oxford, England), 2014-09, Vol.30 (18), p.2684-2685

2014

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Impact of the access tunnel engineering on catalysis is strictly ligand‐specific

The FEBS journal, 2018-04, Vol.285 (8), p.1456-1476

2018

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Dynamics, a Powerful Component of Current and Future in Silico Approaches for Protein Design and Engineering

International journal of molecular sciences, 2020-04, Vol.21 (8), p.2713

2020

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Tools and data services registry: a community effort to document bioinformatics resources

Nucleic acids research, 2016-01, Vol.44 (D1), p.D38

2016

Volltextzugriff (PDF)

Computational Analysis of Protein Tunnels and Channels

Methods in molecular biology (Clifton, N.J.), 2018, Vol.1685, p.25

2018

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Engineering Enzyme Stability and Resistance to an Organic Cosolvent by Modification of Residues in the Access Tunnel

Angewandte Chemie (International ed.), 2013-02, Vol.52 (7), p.1959-1963

International ed. in English, 2013

Volltextzugriff (PDF)

Substrate specificity of haloalkane dehalogenases

Biochemical journal, 2011-04, Vol.435 (2), p.345-354

2011

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Divide-and-conquer approach to study protein tunnels in long molecular dynamics simulations

MethodsX, 2023-01, Vol.10, p.101968-101968, Article 101968

2023

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Mechanism-Based Discovery of Novel Substrates of Haloalkane Dehalogenases Using in Silico Screening

Journal of chemical information and modeling, 2015-01, Vol.55 (1), p.54-62

2015

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Evolutionary Analysis As a Powerful Complement to Energy Calculations for Protein Stabilization

ACS catalysis, 2018-10, Vol.8 (10), p.9420-9428

2018

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Dynamics and hydration explain failed functional transformation in dehalogenase design

Nature chemical biology, 2014-06, Vol.10 (6), p.428

2014

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Gates of Enzymes

Chemical reviews, 2013-08, Vol.113 (8), p.5871-5923

2013

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Maximizing the Efficiency of Multienzyme Process by Stoichiometry Optimization

Chembiochem : a European journal of chemical biology, 2014-09, Vol.15 (13), p.1891-1895

2014

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Enantioselectivity of Haloalkane Dehalogenases and its Modulation by Surface Loop Engineering

Angewandte Chemie (International ed.), 2010-08, Vol.49 (35), p.6111-6115

2010

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Interaction of organic solvents with protein structures at protein-solvent interface

Journal of molecular modeling, 2013-11, Vol.19 (11), p.4701-4711

2013

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PredictSNP2: A Unified Platform for Accurately Evaluating SNP Effects by Exploiting the Different Characteristics of Variants in Distinct Genomic Regions

PLoS computational biology, 2016-05, Vol.12 (5), p.e1004962

2016

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Computational tools for designing and engineering enzymes

CAVER Analyst 2.0: analysis and visualization of channels and tunnels in protein structures and molecular dynamics trajectories

PredictSNP: robust and accurate consensus classifier for prediction of disease-related mutations

CAVER 3.0: a tool for the analysis of transport pathways in dynamic protein structures

HotSpot Wizard 2.0: automated design of site-specific mutations and smart libraries in protein engineering

FireProt: Energy- and Evolution-Based Computational Design of Thermostable Multiple-Point Mutants

Ancestral Haloalkane Dehalogenases Show Robustness and Unique Substrate Specificity

Computational tools for designing and engineering biocatalysts

CAVER: Algorithms for Analyzing Dynamics of Tunnels in Macromolecules

CAVER Analyst 1.0: graphic tool for interactive visualization and analysis of tunnels and channels in protein structures

Impact of the access tunnel engineering on catalysis is strictly ligand‐specific

Dynamics, a Powerful Component of Current and Future in Silico Approaches for Protein Design and Engineering

Tools and data services registry: a community effort to document bioinformatics resources

Computational Analysis of Protein Tunnels and Channels

Engineering Enzyme Stability and Resistance to an Organic Cosolvent by Modification of Residues in the Access Tunnel

Substrate specificity of haloalkane dehalogenases

Divide-and-conquer approach to study protein tunnels in long molecular dynamics simulations

Mechanism-Based Discovery of Novel Substrates of Haloalkane Dehalogenases Using in Silico Screening

Evolutionary Analysis As a Powerful Complement to Energy Calculations for Protein Stabilization

Dynamics and hydration explain failed functional transformation in dehalogenase design

Gates of Enzymes

Maximizing the Efficiency of Multienzyme Process by Stoichiometry Optimization

Enantioselectivity of Haloalkane Dehalogenases and its Modulation by Surface Loop Engineering

Interaction of organic solvents with protein structures at protein-solvent interface

PredictSNP2: A Unified Platform for Accurately Evaluating SNP Effects by Exploiting the Different Characteristics of Variants in Distinct Genomic Regions

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