Selection of a representative set of structures from brookhaven protein data bank

1992 ◽  
Vol 14 (2) ◽  
pp. 265-276 ◽  
Author(s):  
Jorma Boberg ◽  
Tapio Salakoski ◽  
Mauno Vihinen
Keyword(s):  
Protein Data Bank ◽  
Data Bank ◽  
Selection Of

scholarly journals The MORPHEUS protein crystallization screen

2009 ◽  
Vol 42 (6) ◽  
pp. 1035-1042 ◽  
Author(s):  
Fabrice Gorrec
Keyword(s):  
Molecular Biology ◽  
Protein Data Bank ◽  
De Novo ◽  
Protein Crystallization ◽  
Data Bank ◽  
Biological Macromolecules ◽  
Similar Chemical ◽  
Chemical Behaviour ◽  
Crystallization Conditions ◽  
Selection Of

A 96-condition initial screen for protein crystallization, called MORPHEUS, has been developed at the MRC Laboratory of Molecular Biology, Cambridge, England (MRC-LMB). The concept integrates several innovative approaches, such as chemically compatible mixes of potential ligands, new buffer systems and precipitant mixes that also act as cryoprotectants. Instead of gathering a set of crystallization conditions that have already been successful, a selection of molecules frequently observed in the Protein Data Bank (PDB) to co-crystallize with proteins has been made. These have been put together in mixes of similar chemical behaviour and structure, and combined with buffers and precipitant mixes that were also derived from PDB searches, to build the screende novo. Observations made at the MRC-LMB and many practical aspects were also taken into account when formulating the screen. The resulting screen is easy to use, comprehensive yet small, and has already yielded a list of crystallization hits using both known and novel samples. As an indicator of success, the screen has now become one of the standard screens used routinely at the MRC-LMB when searching initial crystallization conditions for biological macromolecules.

scholarly journals Crystallographically correct but confusing presentation of structural models deposited in the Protein Data Bank

2018 ◽  
Vol 74 (9) ◽  
pp. 939-945
Author(s):  
Zbigniew Dauter ◽  
Alexander Wlodawer
Keyword(s):  
Protein Data Bank ◽  
Structural Biology ◽  
Data Bank ◽  
Biologically Active ◽  
Group Symmetry ◽  
Optimal Placement ◽  
Crystal Unit Cell ◽  
Novel Drugs ◽  
Correct Representation ◽  
Selection Of

The Protein Data Bank (PDB) constitutes a collection of the available atomic models of macromolecules and their complexes obtained by various methods used in structural biology, but chiefly by crystallography. It is an indispensable resource for all branches of science that deal with the structures of biologically active molecules, such as structural biology, bioinformatics, the design of novel drugs etc. Since not all users of the PDB are familiar with the methods of crystallography, it is important to present the results of crystallographic analyses in a form that is easy to interpret by nonspecialists. It is advisable during the submission of structures to the PDB to pay attention to the optimal placement of molecules within the crystal unit cell, to the correct representation of oligomeric assemblies and to the proper selection of the space-group symmetry. Examples of significant departures from these principles illustrate the potential for the misinterpretation of such suboptimally presented crystal structures.

scholarly journals The study of interhelical angles in the structural motifs formed by two helices

2017 ◽  
Vol 12 (1) ◽  
pp. 83-101 ◽  
Author(s):  
Д.А. Тихонов ◽  
D.A. Tikhonov
Keyword(s):  
Statistical Analysis ◽  
Protein Data Bank ◽  
Entire Range ◽  
Structural Organization ◽  
Protein Structures ◽  
Data Bank ◽  
Acute Angle ◽  
Spatial Structures ◽  
Pass Through ◽  
Selection Of

In this paper a statistical analysis of distributions of inter-helical angles in pairs of consecutive and connected α-helices in spatial structures of proteins is presented. A number of rules for selection of the helical pairs from a set of protein structures obtained from the Protein Data Bank (PDB) were developed. The set of helical pairs has been analyzed for the purpose of classification and finding out the features of protein structural organization. All pairs of connected helices were divided into three subsets according to the criterion of crossing of projections of the helices on parallel planes, which pass through the axes of the helices. It is shown that the distribution of all types of helical pairs, whose projections do not cross each others, covers almost the entire range of inter-helical angles. The distribution have a single maximum which is close to right angle. Most pairs in this set constitute helical pairs consisting of α- and 310-helices, and most pairs with the crossing projections of helices are helical pairs formed by two α-helices. It is also shown that a great amount of the pairs of connected α-helices has acute angle 20° ≤ φ ≤ 60° between the axes of the helices. The distribution of all types of helical pairs depending on the length of the inter-helical connections was also analyzed. It is shown that the structures with short connections occur most often in all the subsets.

scholarly journals The Protein Data Bank: data distribution and query functionality

2002 ◽  
Vol 58 (s1) ◽  
pp. c214-c214
Author(s):  
W. F. Bluhm ◽  
T. Battistuz ◽  
E. Clingman ◽  
N. Deshpande ◽  
W. Fleri ◽  
...  
Keyword(s):  
Protein Data Bank ◽  
Data Distribution ◽  
Data Bank

FLIPPER: predicting and characterizing linear interacting peptides in the Protein Data Bank

2021 ◽  
pp. 166900
Author(s):  
Alexander Miguel Monzon ◽  
Paolo Bonato ◽  
Marco Necci ◽  
Silvio C.E. Tosatto ◽  
Damiano Piovesan
Keyword(s):  
Protein Data Bank ◽  
Data Bank

scholarly journals Validation and correction of Zn–Cys x His y complexes

2016 ◽  
Vol 72 (10) ◽  
pp. 1110-1118 ◽  
Author(s):  
Wouter G. Touw ◽  
Bart van Beusekom ◽  
Jochem M. G. Evers ◽  
Gert Vriend ◽  
Robbie P. Joosten
Keyword(s):  
Crystal Structures ◽  
Protein Data Bank ◽  
Model Validation ◽  
Data Bank ◽  
Zinc Complexes ◽  
Zinc Ions ◽  
Tetrahedral Complex ◽  
Context Sensitive

Many crystal structures in the Protein Data Bank contain zinc ions in a geometrically distorted tetrahedral complex with four Cys and/or His ligands. A method is presented to automatically validate and correct these zinc complexes. Analysis of the corrected zinc complexes shows that the average Zn–Cys distances and Cys–Zn–Cys angles are a function of the number of cysteines and histidines involved. The observed trends can be used to develop more context-sensitive targets for model validation and refinement.

scholarly journals Protein Data Bank: the single global archive for 3D macromolecular structure data

2018 ◽  
Vol 47 (D1) ◽  
pp. D520-D528 ◽  
Author(s):  
◽  
Stephen K Burley ◽  
Helen M Berman ◽  
Charmi Bhikadiya ◽  
Chunxiao Bi ◽  
...  
Keyword(s):  
Protein Data Bank ◽  
Structure Data ◽  
Data Bank ◽  
Macromolecular Structure
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