1994
DOI: 10.1107/s0907444993011333
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Detection, delineation, measurement and display of cavities in macromolecular structures

Abstract: A computer program,

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Cited by 958 publications
(764 citation statements)
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“…The only obvious differences involve side chain rotamers of several residues (Asn133, Lys134 and Asn135) involved in phosphate interactions. However, the orientations of the two molecules relative to the DNA helical axis are different: molecule A is rotated by ~20° relative to molecule B, resulting in a larger cavity 40 …”
Section: Dam-dna Nonspecific Interactionsmentioning
confidence: 99%
See 2 more Smart Citations
“…The only obvious differences involve side chain rotamers of several residues (Asn133, Lys134 and Asn135) involved in phosphate interactions. However, the orientations of the two molecules relative to the DNA helical axis are different: molecule A is rotated by ~20° relative to molecule B, resulting in a larger cavity 40 …”
Section: Dam-dna Nonspecific Interactionsmentioning
confidence: 99%
“…The only obvious differences involve side chain rotamers of several residues (Asn133, Lys134 and Asn135) involved in phosphate interactions. However, the orientations of the two molecules relative to the DNA helical axis are different: molecule A is rotated by ~20° relative to molecule B, resulting in a larger cavity 40 for molecule A (170 Å 3 ) vs. molecule B (30 Å 3 ) at the interface of protein and DNA. The smaller cavity and the larger buried surface area suggest that the binding mode of molecule B might be closer to a specific binding mode than that if molecule A.…”
Section: Dam-dna Nonspecific Interactionsmentioning
confidence: 99%
See 1 more Smart Citation
“…Buckle et al (1996) used the program VOID00 (Kleywegt & Jones. 1994) with a probe radius of 0.8 A ; those of Varadarajan and Richards (1992) used a Voronoi analysis.…”
Section: Valine 149 To Alaninementioning
confidence: 99%
“…Although of similar areas (20–30 Å 2 ), the open triangular apertures of 2 resultantly present a less equilateral surface than 1 . Void volumes, calculated using VOIDOO,16 revealed cavities of 282 Å 3 for 1 and 423 Å 3 for 2 . These volumes are approximately ten times larger than those of the M II 4 L 4 tetrahedra formed from the same triamines using 2‐formylpyridine 17…”
mentioning
confidence: 99%