Exploring Protein Sequence Space Using Computationally Directed Recombination [PDF]
, 2006 Evolution has provided us with many protein sequences. However, these sequences represent a very small fraction of the possible sequences. In the laboratory, scientists have explored areas of sequence space not represented by natural proteins both to ...
Meyer, Michelle Margaret
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Statistical Models of the Protein Fitness Landscape: Applications to Protein Evolution and Engineering [PDF]
, 2012 Understanding the protein fitness landscape is important for describing how natural proteins evolve and for engineering new proteins with useful properties.
Romero, Philip Anthony
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BMC Bioinformatics, 2021 Background The identification of protein families is of outstanding practical importance for in silico protein annotation and is at the basis of several bioinformatic resources.
Elena Tea Russo +2 more
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Coevolutionary Analysis of Protein Subfamilies by Sequence Reweighting
Entropy, 2019 Extracting structural information from sequence co-variation has become a common computational biology practice in the recent years, mainly due to the availability of large sequence alignments of protein families.
Duccio Malinverni, Alessandro Barducci
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Computational Protein Design Force Field Optimization: A Negative Design Approach [PDF]
, 2007 An accurate force field is essential to computational protein design and protein folding studies. Proper force field tuning is problematic, however, due in part to the incomplete modeling of the unfolded state.
Alvizo, Oscar
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iSeqSearch: incremental protein search for iBlast/iMMSeqs2/iDiamond [PDF]
PeerJBackground The advancement of sequencing technology has led to a rapid increase in the amount of DNA and protein sequence data; consequently, the size of genomic and proteomic databases is constantly growing.
Hyunwoo Yoo +5 more
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SeqCP: A sequence-based algorithm for searching circularly permuted proteins
Computational and Structural Biotechnology Journal, 2023 Circular permutation (CP) is a protein sequence rearrangement in which the amino- and carboxyl-termini of a protein can be created in different positions along the imaginary circularized sequence.
Chi-Chun Chen +4 more
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Development and Validation of Optimization Methods for the Design of Protein Sequences and Combinatorial Libraries [PDF]
, 2009 To facilitate the design of protein sequences with desired properties, simulation techniques have been developed to allow large portions of amino acid sequence space to be evaluated by computer.
Allen, Benjamin Daniel
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Analysis of protein chameleon sequence characteristics [PDF]
Bioinformation, 2009 Conversion of local structural state of a protein from an alpha-helix to a beta-strand is usually associated with a major change in the tertiary structure. Similar changes were observed during the self assembly of amyloidogenic proteins to form fibrils, which are implicated in severe diseases conditions, e.g., Alzheimer disease. Studies have emphasized
Ghozlane, Amine +3 more
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Species-specific analysis of protein sequence motifs using mutual information
BMC Bioinformatics, 2005 Background Protein sequence motifs are by definition short fragments of conserved amino acids, often associated with a specific function. Accordingly protein sequence profiles derived from multiple sequence alignments provide an alternative description ...
Weckwerth Wolfram +3 more
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