Biophysics of protein evolution and evolutionary protein biophysics
The study of molecular evolution at the level of protein-coding genes often entails comparing
large datasets of sequences to infer their evolutionary relationships. Despite the importance …
large datasets of sequences to infer their evolutionary relationships. Despite the importance …
Protein folding thermodynamics and dynamics: where physics, chemistry, and biology meet
E Shakhnovich - Chemical reviews, 2006 - ACS Publications
As was noted in our recent review, 1 the protein folding field underwent a cyclic
development. Initially, protein folding was viewed as a strictly experimental field belonging to …
development. Initially, protein folding was viewed as a strictly experimental field belonging to …
New quantitative descriptors of amino acids based on multidimensional scaling of a large number of physical–chemical properties
MS Venkatarajan, W Braun - Molecular modeling annual, 2001 - Springer
We derive new quantitative descriptors for the 20 naturally occurring amino acids based on
multidimensional scaling of 237 physical–chemical properties. We show that a five …
multidimensional scaling of 237 physical–chemical properties. We show that a five …
[HTML][HTML] From genotypes to organisms: State-of-the-art and perspectives of a cornerstone in evolutionary dynamics
Understanding how genotypes map onto phenotypes, fitness, and eventually organisms is
arguably the next major missing piece in a fully predictive theory of evolution. We refer to this …
arguably the next major missing piece in a fully predictive theory of evolution. We refer to this …
Modeling evolutionary landscapes: mutational stability, topology, and superfunnels in sequence space
Random mutations under neutral or near-neutral conditions are studied by considering
plausible evolutionary trajectories on “neutral nets”—ie, collections of sequences …
plausible evolutionary trajectories on “neutral nets”—ie, collections of sequences …
Rational evolutionary design: the theory of in vitro protein evolution
Publisher Summary Directed evolution uses a combination of powerful search techniques to
generate proteins with the improved properties. The chapter focuses on controlling the …
generate proteins with the improved properties. The chapter focuses on controlling the …
How many protein sequences fold to a given structure? A coevolutionary analysis
Quantifying the relationship between protein sequence and structure is key to understanding
the protein universe. A fundamental measure of this relationship is the total number of amino …
the protein universe. A fundamental measure of this relationship is the total number of amino …
Protein design at the interface of the pre-biotic and biotic worlds
LM Longo, M Blaber - Archives of biochemistry and biophysics, 2012 - Elsevier
“Proteogenesis”(the origin of proteins) is a likely key event in the unsolved problem of
biogenesis (the origin of life). The raw material for the very first proteins comprised the …
biogenesis (the origin of life). The raw material for the very first proteins comprised the …
Thoroughly sampling sequence space: Large‐scale protein design of structural ensembles
SM Larson, JL England, JR Desjarlais… - Protein …, 2002 - Wiley Online Library
Modeling the inherent flexibility of the protein backbone as part of computational protein
design is necessary to capture the behavior of real proteins and is a prerequisite for the …
design is necessary to capture the behavior of real proteins and is a prerequisite for the …
Enumerating designing sequences in the HP model
A Irbäck, C Troein - Journal of Biological Physics, 2002 - Springer
The hydrophobic/polar HP model on the square lattice has been widely used toinvestigate
basics of protein folding. In the cases where all designing sequences (sequences with …
basics of protein folding. In the cases where all designing sequences (sequences with …