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Journal Article
PLoS Genetics, ISSN 1553-7390, 04/2019, Volume 15, Issue 4, pp. e1008079 - e1008079
Characterizing the fitness landscape, a representation of fitness for a large set of genotypes, is key to understanding how genetic information is interpreted... 
RECOMBINATION | IN-VITRO | EVOLUTION | PREDICTABILITY | EPISTATIC INTERACTIONS | PROTEIN-STRUCTURE | SIGN EPISTASIS | SPECIATION | GENETICS & HEREDITY | SELECTION | MUTATIONAL PATHWAYS | Fungal Proteins - chemistry | Saccharomyces cerevisiae - genetics | Phylogeny | Amino Acids - genetics | Saccharomyces cerevisiae - metabolism | Amino Acids - metabolism | Genes, Fungal | Hydro-Lyases - metabolism | Hydro-Lyases - genetics | Yeasts - metabolism | Amino Acid Sequence | Models, Molecular | Genotype | Fungal Proteins - genetics | Saccharomyces cerevisiae Proteins - genetics | Yeasts - genetics | Genetic Fitness | Epistasis, Genetic | Saccharomyces cerevisiae Proteins - metabolism | Models, Genetic | Hydro-Lyases - chemistry | Amino Acid Substitution | Evolution, Molecular | Fungal Proteins - metabolism | Saccharomyces cerevisiae Proteins - chemistry | Enzymes | Physiological aspects | Genetic research | Amino acids | Fitness (Genetics) | Genetic aspects | Research | Biological assay | Methods | Visualization | Laboratories | Funding | Genomics | Epistasis | Genomes | Biology | Proteins | Genotype & phenotype | Histidine | Evolution | Genetics | Software | Mutation | Bioinformatics | Supervision | Genotypes | Fitness | Index Medicus | Variant genotypes | Protein sequencing | Evolutionary genetics | Sign epistasis | Fitness epistasis | Saccharomyces cerevisiae | Amino acid substitution
Journal Article
Nucleic Acids Research, ISSN 0305-1048, 1/2009, Volume 37, Issue suppl_1, pp. D342 - D346
We propose here KineticDB, a systematically compiled database of protein folding kinetics, which contains about 90 unique proteins. The main goal of the... 
RATES | DESIGN | SINGLE-DOMAIN PROTEINS | AMINO-ACID-SEQUENCE | NUCLEI | BIOCHEMISTRY & MOLECULAR BIOLOGY | CONTACT ORDER | SIZE | SECONDARY STRUCTURE | 2-STATE PROTEINS | PREDICTION | Protein Structure, Tertiary | Kinetics | Peptides - chemistry | Databases, Protein | Protein Folding | Index Medicus
Journal Article
PLoS ONE, ISSN 1932-6203, 08/2009, Volume 4, Issue 8, pp. e6476 - e6476
There are several important questions on the coupling between properties of the protein shape and the rate of protein folding. We have studied a series of... 
MULTIDISCIPLINARY SCIENCES | Protein Conformation | Protein Folding | Proteins - chemistry | Comparative analysis | Protein folding | Correlation coefficient | Correlation coefficients | Biochemistry | Gyration | Data bases | Intermediates | Trends | Kinetics | Coupling | Surface area | Cross sections | Folding | Index Medicus
Journal Article
Bioinformatics, ISSN 1367-4803, 11/2018, Volume 34, Issue 21, pp. 3653 - 3658
Abstract Motivation Computational prediction of the effect of mutations on protein stability is used by researchers in many fields. The utility of the... 
MODIFIED FOLDX PROTOCOL | PROTEIN STABILITY | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | SERVER | SEQUENCE | BIOCHEMICAL RESEARCH METHODS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | Original Papers
Journal Article
Nucleic acids research, ISSN 0305-1048, 2013, Volume 41, Issue W1, pp. W459 - 464
Journal Article
PLoS Computational Biology, ISSN 1553-734X, 10/2010, Volume 6, Issue 10
  Intrinsically disordered regions serve as molecular recognition elements, which play an important role in the control of many cellular processes and... 
Proteins | Amino acids | Kinases | Data bases | Deoxyribonucleic acid--DNA
Journal Article
Proteins: Structure, Function, and Bioinformatics, ISSN 0887-3585, 02/2008, Volume 70, Issue 2, pp. 329 - 332
We have demonstrated that, among proteins of the same size, α/β proteins have on the average a greater number of contacts per residue due to their more compact... 
compactness | protein packing | number of contacts per residue | structural class | Number of contacts per residue | Structural class | Protein packing | Compactness | EVOLUTION | BIOPHYSICS | SEQUENCES | PACKING DENSITY | BIOCHEMISTRY & MOLECULAR BIOLOGY | VOLUME | Protein Conformation | Protein Folding | Proteins - chemistry | Index Medicus
Journal Article
Journal of Bioinformatics and Computational Biology, ISSN 0219-7200, 04/2006, Volume 4, Issue 2, pp. 597 - 608
Archaea, bacteria and eukaryotes represent the main kingdoms of life. Is there any trend for amino acid compositions of proteins found in full genomes of... 
Proteome | Viruses | Eukaryotes | Uniform usage of codone | Amino Acid Sequence | Sequence Analysis, Protein - methods | Proteome - genetics | Species Specificity | Humans | Molecular Sequence Data | Proteome - chemistry | Sequence Homology, Amino Acid | Sequence Alignment - methods | Animals | Codon | Conserved Sequence | Evolution, Molecular
Journal Article
Journal of Bioinformatics and Computational Biology, ISSN 0219-7200, 2008, Volume 6, Issue 4, pp. 667 - 680
We have demonstrated here that protein compactness, which we define as the ratio of the accessible surface area of a protein to that of the ideal sphere of the... 
Multi-state kinetics | Sphericity | Structural class | Protein packing | Compactness | Two-state kinetics | Models, Chemical | Computer Simulation | Models, Molecular | Protein Conformation | Proteins - chemistry | Protein Folding | Proteins - ultrastructure
Journal Article
Journal of Bioinformatics and Computational Biology, ISSN 0219-7200, 2008, Volume 6, Issue 5, pp. 1035 - 1047
We suggest an algorithm that inputs a protein sequence and outputs a decomposition of the protein chain into a regular part including secondary structures and... 
Disordered region | Window size | Loops | Secondary structure | Flexible region | Amino Acid Sequence | Sequence Alignment - methods | Sequence Analysis, Protein - methods | Algorithms | Models, Chemical | Computer Simulation | Models, Molecular | Protein Conformation | Proteins - chemistry | Proteins - ultrastructure
Journal Article