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  2. FoldX - Wikipedia

    en.wikipedia.org/wiki/FoldX

    For protein-protein interactions, or protein-DNA interactions FoldX calculates ∆∆G of interaction : ∆∆G ab = ∆G ab - (∆G a + ∆G b ) + ∆G kon + ∆S sc ∆G kon reflects the effect of electrostatic interactions on the k on . ∆S sc is the loss of translational and rotational entropy upon making the complex.

  3. Multiple sequence alignment - Wikipedia

    en.wikipedia.org/wiki/Multiple_sequence_alignment

    Alignments highlight mutation events such as point mutations (single amino acid or nucleotide changes), insertion mutations and deletion mutations, and alignments are used to assess sequence conservation and infer the presence and activity of protein domains, tertiary structures, secondary structures, and individual amino acids or nucleotides.

  4. Neutral network (evolution) - Wikipedia

    en.wikipedia.org/wiki/Neutral_network_(evolution)

    Neutral networks are a subset of the sequences in sequence space that have equivalent function, and so form a wide, flat plateau in a fitness landscape. Neutral evolution can therefore be visualised as a population diffusing from one set of sequence nodes, through the neutral network, to another cluster of sequence nodes.

  5. Nearly neutral theory of molecular evolution - Wikipedia

    en.wikipedia.org/wiki/Nearly_neutral_theory_of...

    In this case, the faster rate of neutral evolution in proteins expected in small populations (due to a more lenient threshold for purging deleterious mutations) is offset by longer generation times (and vice versa), but in large populations with short generation times, noncoding DNA evolves faster while protein evolution is retarded by ...

  6. De novo protein structure prediction - Wikipedia

    en.wikipedia.org/wiki/De_novo_protein_structure...

    De novo protein structure prediction methods attempt to predict tertiary structures from sequences based on general principles that govern protein folding energetics and/or statistical tendencies of conformational features that native structures acquire, without the use of explicit templates. Research into de novo structure prediction has been ...

  7. Protein structure prediction - Wikipedia

    en.wikipedia.org/wiki/Protein_structure_prediction

    A protein structure prediction method must explore the space of possible protein structures which is astronomically large. These problems can be partially bypassed in "comparative" or homology modeling and fold recognition methods, in which the search space is pruned by the assumption that the protein in question adopts a structure that is ...

  8. Homology modeling - Wikipedia

    en.wikipedia.org/wiki/Homology_modeling

    Homology model of the DHRS7B protein created with Swiss-model and rendered with PyMOL. Homology modeling, also known as comparative modeling of protein, refers to constructing an atomic-resolution model of the "target" protein from its amino acid sequence and an experimental three-dimensional structure of a related homologous protein (the "template").

  9. Directed evolution - Wikipedia

    en.wikipedia.org/wiki/Directed_evolution

    A drawback of this is that even when the structure and mechanism of action of the protein are well known, the change due to mutation is still difficult to predict. Therefore, an advantage of DE is that there is no need to understand the mechanism of the desired activity or how mutations would affect it. [30]