Conformation families of protein fragments in multidimensional torsion-angle space

Pavelčík, F.; Pavelčíková, Pamela

doi:10.1107/s0907444907045921

Cited by 4 publications

(9 citation statements)

References 17 publications

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“…Searching for a-helices and other tripeptides. The chain tracing is initiated by finding seven-residue -helices or the three most common tripeptides (Pavelcik & Pavelcikova, 2007) in the density by evaluating a weighted sum f( 0 ) of the modified density 0 at the atomic sites and also at points where, because of steric clashes with the fragments in question, no density is to be expected ('holes'). The weights are set to the atomic numbers, except that for C (which would be absent for a glycine) the weight is set to 4 and for a 'hole' it is set to À2.…”

Section: Autotracingmentioning

confidence: 99%

Experimental phasing with SHELXC/D/E: combining chain tracing with density modification

Sheldrick

2010

Acta Crystallogr D Biol Crystallogr

1,092

929

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The programsSHELXC, SHELXDandSHELXEare designed to provide simple, robust and efficient experimental phasing of macromolecules by the SAD, MAD, SIR, SIRAS and RIP methods and are particularly suitable for use in automated structure-solution pipelines. This paper gives a general account of experimental phasing using these programs and describes the extension of iterative density modification in SHELXEby the inclusion of automated protein main-chain tracing. This gives a good indication as to whether the structure has been solved and enables interpretable maps to be obtained from poorer starting phases. The autotracing algorithm starts with the location of possible seven-residue α-helices and common tripeptides. After extension of these fragments in both directions, various criteria are used to decide whether to accept or reject the resulting poly-Ala traces. Noncrystallographic symmetry (NCS) is applied to the traced fragments, not to the density. Further features are the use of a `no-go' map to prevent the traces from passing through heavy atoms or symmetry elements and a splicing technique to combine the best parts of traces (including those generated by NCS) that partly overlap.

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Section: Autotracingmentioning

confidence: 99%

Experimental phasing with SHELXC/D/E: combining chain tracing with density modification

Sheldrick

2010

Acta Crystallogr D Biol Crystallogr

1,092

929

View full text Add to dashboard Cite

show abstract

“…This fragment contains three peptide groups, two pairs of (', ) torsion angles, four CA atoms, two CB atoms and is approximately of tripeptide size. Based on previous statistics (Pavelcik & Pavelcikova, 2007), the number of conformation families seems to be reasonable and the errors introduced by the assumption of fixed bond lengths and fixed bond angles do not appear to be large. The fragment was designed to be a compromise between size and number of conformers.…”

Section: Molecular Fragment and Conformer Tablesmentioning

confidence: 67%

“…Each flexible torsion represents one search dimension. The recent data used for calculations and stored in the NUT program are presented in Tables 2 and 3 of Pavelcik & Pavelcikova (2007); the number of conformers in the program is limited to 16.…”

Section: Molecular Fragment and Conformer Tablesmentioning

confidence: 99%

“…For this reason, the fragment radius represents the critical parameter for the PRCTF. Experimental fragment radii were analyzed for crystal structures from a protein database, using the same set as were used for analysis of the conformation families (Pavelcik & Pavelcikova, 2007) (2002). The radii are presented in Table 1.…”

Section: Molecular Fragment and Conformer Tablesmentioning

confidence: 99%

“…Searches have to be limited to preferred conformations, known as conformation families. Conformation families of polypeptides at higher dimensions have been established (Pavelcik & Vanco, 2006;Pavelcik & Pavelcikova, 2007) by the direct mapping of multidimensional periodic torsion-angle space. This opened up a way to build macromolecular structures at lower resolutions using oligopeptides by the PRCTF.…”

Section: Introductionmentioning

confidence: 99%

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Performance of phased rotation, conformation and translation function: accurate protein model building with tripeptidic and tetrapeptidic fragments

Pavelčík

Václavík

2010

Acta Crystallogr D Biol Cryst

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The automatic building of protein structures with tripeptidic and tetrapeptidic fragments was investigated. The oligopeptidic conformers were positioned in the electron-density map by a phased rotation, conformation and translation function and refined by a real-space refinement. The number of successfully located fragments lay within the interval 75-95% depending on the resolution and phase quality. The overlaps of partially located fragments were analyzed. The correctly positioned fragments were connected into chains. Chains formed in this way were extended directly into the electron density and a sequence was assigned. In the initial stage of the model building the number of located fragments was between 60% and 95%, but this number could be increased by several cycles of reciprocal-space refinement and automatic model rebuilding. A nearly complete structure can be obtained on the condition that the resolution is reasonable. Computer graphics will only be needed for a final check and small corrections.

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Application of constrained real-space refinement of flexible molecular fragments to automatic model building of RNA structures

Pavelčík

2012

J Appl Cryst

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New methods have been developed for locating phosphate groups and nucleic acid bases in the electron density of RNA structures. These methods utilize a constrained real-space refinement of molecular fragments and a phased rotation-conformation-translation function. Real-space refinement has also contributed to the improvement of the bone/base method of RNA model building and to redesigning the method of building double helices in nucleic acid structures. This improvement is reflected in the increased accuracy of the model building and the ability to better distinguish between correct and false solutions. A program, RSR, was created, and the programs NUT, HEL and DHL were upgraded and organized into a program system, which is CCP4 oriented. Source codes will also be released.

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Conformation families of protein fragments in multidimensional torsion-angle space

Cited by 4 publications

References 17 publications

Experimental phasing with SHELXC/D/E: combining chain tracing with density modification

Experimental phasing with SHELXC/D/E: combining chain tracing with density modification

Performance of phased rotation, conformation and translation function: accurate protein model building with tripeptidic and tetrapeptidic fragments

Application of constrained real-space refinement of flexible molecular fragments to automatic model building of RNA structures

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