Pex, analytical tools for PDB files. I. GF‐Pex: Basic file to describe a protein

Thomas, A. G.; Bouffioux, Olivier; Geeurickx, Dominique; Brasseur, Robert

doi:10.1002/1097-0134(20010401)43:1<28::aid-prot1014>3.3.co;2-d

Cited by 7 publications

(15 citation statements)

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“…These values are used as 100% for the scoring of amino acid stability in peptide structures. They have been calculated on 494 refined PDB structures17 by evaluating all atomic interactions between nonbound atoms using a cut off distance of 10 Å. Atom–atom MFP functions were previously calibrated on the same protein structure database, using 81 different types of atom couples, and Pex databases were used to collect and cluster data per residue 18. The references are thus the mean MFP values of amino acids in folded proteins.…”

Section: Methodsmentioning

confidence: 99%

Prediction of peptide structure: How far are we?

et al. 2006

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Rational design of peptides is a challenge, which would benefit from a better knowledge of the rules of sequence-structure-function relationships. Peptide structures can be approached by spectroscopy and NMR techniques but data from these approaches too frequently diverge. Structures can also be calculated in silico from primary sequence information using three algorithms: Pepstr, Robetta, and PepLook. The most recent algorithm, PepLook introduces indexes for evaluating structural polymorphism and stability. For peptides with converging experimental data, calculated structures from PepLook and, to a lesser extent from Pepstr, are close to NMR models. The PepLook index for polymorphism is low and the index for stability points out possible binding sites. For peptides with divergent experimental data, calculated and NMR structures can be similar or, can be different. These differences are apparently due to polymorphism and to different conditions of structure assays and calculations. The PepLook index for polymorphism maps the fragments encoding disorder. This should provide new means for the rational design of peptides.

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Section: Methodsmentioning

confidence: 99%

Prediction of peptide structure: How far are we?

et al. 2006

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“…We used the same database of 593 nonredundant proteins58 as in our previous analysis of aromatic pairs1 and the same Pex files 59…”

Section: Methodsmentioning

confidence: 99%

Aromatic side‐chain interactions in proteins: Near‐ and far‐sequence Tyr‐X pairs

Meurisse¹,

Brasseur²,

Thomas³

2003

Proteins

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In the present study, an extensive analysis of the aromatic Tyr-X interactions is performed on a data set of 593 PDB structures, X being Phe, His, Tyr, and Trp. The nonredundant Tyr-X pairs (2645) were retained and separated by both the residue distance in the sequence and the secondary structures they bridge. Similar to the Phe-X and His-X pairs, the far-sequence Tyr-X pairs (X partner > five apart in the sequence: 74%) show comparable secondary structures and conformers for either type of X partner, in contrast with the near-sequence Tyr-X pairs (26%). As the Phe-X pairs, the near-sequence Tyr-X pairs stabilize secondary structures, mainly the alpha- helices (positions 1, 3, and 4) and the beta-strands (position 2). Like the Phe-X and His-X pairs, most far-sequence Tyr-X pairs (34%) bridge beta-strands and only 11% bridge helices. As for the Phe-X and the His-X pairs, the X partners of the far-sequence Tyr-X pairs are frequently "above" the tyrosine ring with tilted and normal rings, whereas the X partner of the near-sequence Tyr-X pairs gradually moves from the "aside" to the "above" location, together with a progressive decrease of normal and increase of parallel rings, respectively. Unlike the His-X pairs, the interactions of the hetroatom in Tyr-X pairs are only favored with a sequence position +4 and over, owing to the spatial accessibility of the heteroatom.

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“…The identity varies from 5% to 28% with an average value around 15%, below the nominal threshold for a reliable sequence alignment [ 21 ]. Detection of residues in interaction in the structures was done using the PEX software [ 22 ]. Interactions are classified depending on the nature of the amino acids implicated, that is to say hydrophobic (Ala, Cys, Phe, Gly, His, Ile, Leu, Met, Val, Trp, Tyr, Pro), hydrophilic (Asp, Glu, Arg, Lys, His, Asn, Gln, Ser, Thr, Tyr), charged (Asp, Glu, Arg, Lys, His) and aromatic (Phe, His, Tyr, Trp).…”

Section: Resultsmentioning

confidence: 99%

“…The interactions were computed from PDB files with the PEX software[ 22 ]. Previously, the PDB files corresponding to the structures were renumbered, so that spatially equivalent residues (i.e.…”

Section: Methodsmentioning

confidence: 99%