Robust enzyme design: Bioinformatic tools for improved protein stability

Sperm-specific glyceraldehyde-3-phosphate dehydrogenase is stabilized by additional proline residues and an interdomain salt bridge

(2014) Mikhail Kuravsky et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Computational tools for designing and engineering enzymes

(2014) Jiri Damborsky et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

pocketZebra: a web-server for automated selection and classification of subfamily-specific binding sites by bioinformatic analysis of diverse protein families

(2014) Dmitry Suplatov et al.   NUCLEIC ACIDS RESEARCH

Computational Design of a pH Stable Enzyme: Understanding Molecular Mechanism of Penicillin Acylase's Adaptation to Alkaline Conditions

(2014) Dmitry Suplatov et al.   PLoS One

Stabilizing biocatalysts

(2013) Andreas S. Bommarius et al.   CHEMICAL SOCIETY REVIEWS

Structure- and sequence-analysis inspired engineering of proteins for enhanced thermostability

(2013) Hein J Wijma et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Modulating protein stability - directed evolution strategies for improved protein function

(2013) Raymond D. Socha et al.   FEBS Journal

Zebra: a web server for bioinformatic analysis of diverse protein families

(2013) Dmitry Suplatov et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Bioinformatic analysis of protein families for identification of variable amino acid residues responsible for functional diversity

(2013) Dmitry Suplatov et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

GroEL/ES Buffering and Compensatory Mutations Promote Protein Evolution by Stabilizing Folding Intermediates

(2013) Kirsten T. Wyganowski et al.   JOURNAL OF MOLECULAR BIOLOGY

Biocatalysis in Organic Chemistry and Biotechnology: Past, Present, and Future

(2013) Manfred T. Reetz   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Navigating the protein fitness landscape with Gaussian processes

(2013) P. A. Romero et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Strategies for Stabilization of Enzymes in Organic Solvents

(2013) Veronika Stepankova et al.   ACS Catalysis

Improved Thermostability of Clostridium thermocellum Endoglucanase Cel8A by Using Consensus-Guided Mutagenesis

(2012) Michael Anbar et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Improving the thermostability of alpha-amylase by combinatorial coevolving-site saturation mutagenesis

(2012) Chenghua Wang et al.   BMC BIOINFORMATICS

Protein engineering of a thermostable polyol dehydrogenase

(2012) H. Wulf et al.   ENZYME AND MICROBIAL TECHNOLOGY

Structure-based engineering of histidine residues in the catalytic domain of α-amylase from Bacillus subtilis for improved protein stability and catalytic efficiency under acidic conditions

(2012) Haiquan Yang et al.   JOURNAL OF BIOTECHNOLOGY

Stabilizing Proteins from Sequence Statistics: The Interplay of Conservation and Correlation in Triosephosphate Isomerase Stability

(2012) Brandon J. Sullivan et al.   JOURNAL OF MOLECULAR BIOLOGY

Engineering the third wave of biocatalysis

(2012) U. T. Bornscheuer et al.   NATURE

Bioinformatic analysis of alpha/beta-hydrolase fold enzymes reveals subfamily-specific positions responsible for discrimination of amidase and lipase activities

(2012) D. A. Suplatov et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Advanced evolutionary molecular engineering to produce thermostable cellulase by using a small but efficient library

(2012) Y. Ito et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Modular exchange of substrate-binding loops alters both substrate and cofactor specificity in a member of the aldo-keto reductase superfamily

(2012) E. Campbell et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Engineering catalytic properties and thermal stability of plant formate dehydrogenase by single-point mutations

(2012) A. A. Alekseeva et al.   PROTEIN ENGINEERING DESIGN & SELECTION

COMPUTATIONAL TOOLS FOR RATIONAL PROTEIN ENGINEERING OF ALDOLASES

(2012) Michael Widmann et al.   Computational and Structural Biotechnology Journal

Utilizing natural diversity to evolve protein function: applications towards thermostability

(2011) Megan F Cole et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Protein 3D Structure Computed from Evolutionary Sequence Variation

(2011) Debora S. Marks et al.   PLoS One

Understanding protein non-folding

(2010) Vladimir N. Uversky et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Thermostabilization of an esterase by alignment-guided focussed directed evolution

(2010) Helge Jochens et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Improvement of Bacillus circulans β-amylase activity attained using the ancestral mutation method

(2010) Kan Yamashiro et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Correlated Mutations: A Hallmark of Phenotypic Amino Acid Substitutions

(2010) Andreas Kowarsch et al.   PLoS Computational Biology

Directed Evolution of Serum Paraoxonase PON3 by Family Shuffling and Ancestor/Consensus Mutagenesis, and Its Biochemical Characterization

(2009) Olga Khersonsky et al.   BIOCHEMISTRY

Stability effects of mutations and protein evolvability

(2009) Nobuhiko Tokuriki et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

A family of thermostable fungal cellulases created by structure-guided recombination

(2009) P. Heinzelman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rational pH-engineering of the thermostable xylanase based on computational model

(2009) Liangwei Liu et al.   PROCESS BIOCHEMISTRY

Correlated mutation analyses on super-family alignments reveal functionally important residues

(2009) Remko K. P. Kuipers et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

A   -barrel built by the combination of fragments from different folds

(2008) T. A. M. Bharat et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Thermostable variants constructed via the structure-guided consensus method also show increased stability in salts solutions and homogeneous aqueous-organic media

(2008) E. Vazquez-Figueroa et al.   PROTEIN ENGINEERING DESIGN & SELECTION

How Protein Stability and New Functions Trade Off

(2008) Nobuhiko Tokuriki et al.   PLoS Computational Biology