an ab initio and density functional theory (dft) study about conformational analysis of tripeptide model hco−gly−l−ile−gly−nh2 is presented. the tripeptide was scanned about initial, central, and final residues, separately while for every scanning procedure the two other residues had been kept in the β conformation and side chain (sc) dihedral angles were maintained on the gauche− (g‾) state (χ...

MERA (Maximum Entropy Ramachandran map Analysis from NMR data) is a new webserver that generates residue-by-residue Ramachandran map distributions for disordered proteins or disordered regions in proteins on the basis of experimental NMR parameters. As input data, the program currently utilizes up to 12 different parameters. These include three different types of short-range NOEs, three types o...

The Protein Data Bank (PDB) [3] is the most important depository of protein structural information, containing more than 42,000 deposited entries today. Because of its inhomogeneous structure, its fully automated processing is almost impossible. In a previous work, we cleaned and re-structured the entries in the Protein Data Bank, and from the result we have built the RS-PDB database [11]. Usin...

A Ramachandran plot is a visual representation of the main-chain conformational tendencies of an amino acid. Despite forty years of research, the shape of Ramachandran plots is still a matter of debate. The issue in making a Ramachandran plot based on experimental data is deciding whether sparse data represent genuine conformations. We present here a simple solution to settle the ambiguities of...


 A few years ago, validating proteins to see if they were good or bad was a process that took years. With the creation of Ramachandran Graph evaluates protein structures through angles φ (phi) and ψ (psi), this task became less onerous. evolution computing bioinformatics, platforms have been created generate graphs in an online manner, however, high degree usability complexity. The system...

Since the first years of structural biology, Ramachandran map has provided a simple definition curvilinear geometry protein backbone. Its is mainly based on values dihedral angles $$\phi $$ and $$\psi measured between heavy atoms Discontinuities in angle are observed, particularly region $$\beta -strand secondary structure. We introduce new pseudo-dihedral involving hydrogen positions instead s...

An analysis of the nature and distribution of disallowed Ramachandran conformations of amino acid residues observed in high resolution protein crystal structures has been carried out. A data set consisting of 110 high resolution, non-homologous, protein crystal structures from the Brookhaven Protein Data Bank was examined. The data set consisted of a total of 18,708 non-Gly residues, which were...

An analysis of the occurrence of nonglycyl residues in conformations disallowed in the Ramachandran plot is presented. Ser, Asn, Thr, and Cys have the highest propensities to exhibit such conformations, and the branched aliphatic residues the lowest. Residues cluster in five regions and there are some trends in the types of residues and their side-chain conformations (chi(1)) occupying these. M...