PDBFlex: exploring flexibility in protein structures
نویسندگان
چکیده
منابع مشابه
PDBFlex: exploring flexibility in protein structures
The PDBFlex database, available freely and with no login requirements at http://pdbflex.org, provides information on flexibility of protein structures as revealed by the analysis of variations between depositions of different structural models of the same protein in the Protein Data Bank (PDB). PDBFlex collects information on all instances of such depositions, identifying them by a 95% sequence...
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Fast methods for volume based Protein-Protein docking exist (eg. [1] or [4]). However, they employ the rigid-body assumption, and often miss the correct solution. To enhance todays docking algorithms the "induced fit" (comformational changes of a protein during the docking process) must be handled. Flexibility studies can help improving docking algorithms. Flexibility can be considered by enume...
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Protein structures are valuable tools for understanding protein function. However, protein dynamics is also considered a key element in protein function. Therefore, in addition to structural analysis, fully understanding protein function at the molecular level now requires accounting for flexibility. However, experimental techniques that produce both types of information simultaneously are stil...
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Conserved residues forming tightly packed clusters have been shown to be energy hot spots in both protein-protein and protein-DNA complexes. A number of analyses on these clusters of conserved residues (CCRs) have been reported, all pointing to a crucial role that these clusters play in protein function, especially protein-protein and protein-DNA interactions. However, currently there is no pub...
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Background: Establishing theories for designing arbitrary protein structures is complicated and depends on understanding the principles for protein folding, which is affected by applied features. Computer algorithms can reach high precision and stability in computationally designing enzymes and binders by applying informative features obtained from natural structures. Methods: In this study, a ...
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ژورنال
عنوان ژورنال: Nucleic Acids Research
سال: 2015
ISSN: 0305-1048,1362-4962
DOI: 10.1093/nar/gkv1316