PDB Goodies – a web-based GUI to manipulate the Protein Data Bank file

Hussain, A.; Shanthi, V.; Sheik, S. S.; Jeyakanthan, Jeyaraman; Selvarani, Ponnuthai; Sekar, K.

doi:10.1107/s090744490200985x

Cited by 27 publications

(19 citation statements)

References 2 publications

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“…The PISA (http://www.ebi.ac.uk/pdbe/prot int/pistart.html) web server [58] was used to analyze the interfaces and quaternary structures. In house server PDB Goodies [59] was used for some calculations in the pdb file. The figures were generated using PyMOL (DeLano Scientific; http://www.pymol.org).…”

Section: Sequence and Structure Analysismentioning

confidence: 99%

Structure of SAICAR synthetase from Pyrococcus horikoshii OT3: Insights into thermal stability

Manjunath

Kanaujia

Kanagaraj

et al. 2013

International Journal of Biological Macromolecules

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Section: Sequence and Structure Analysismentioning

confidence: 99%

Structure of SAICAR synthetase from Pyrococcus horikoshii OT3: Insights into thermal stability

Manjunath

Kanaujia

Kanagaraj

et al. 2013

International Journal of Biological Macromolecules

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“…Figures were prepared using PyMOL (DeLano, 2005) and MOLSCRIPT (Kraulis, 1991). Average B factors were calculated using the web-based program PDB GOODIES (Hussain et al, 2002).…”

Section: Gal1-3galmentioning

confidence: 99%

Structural studies on peanut lectin complexed with disaccharides involving different linkages: further insights into the structure and interactions of the lectin

Natchiar

Oruganti

Mitra

et al. 2006

Acta Crystallogr D Biol Crystallogr

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Crystal structures of peanut lectin complexed with Galbeta1-3Gal, methyl-T-antigen, Galbeta1-6GalNAc, Galalpha1-3Gal and Galalpha1-6Glc and that of a crystal grown in the presence of Galalpha1-3Galbeta1-4Gal have been determined using data collected at 100 K. The use of water bridges as a strategy for generating carbohydrate specificity was previously deduced from the complexes of the lectin with lactose (Galbeta1-4Glc) and T-antigen (Galbeta1-3GalNAc). This has been confirmed by the analysis of the complexes with Galbeta1-3Gal and methyl-T-antigen (Galbeta1-3GalNAc-alpha-OMe). A detailed analysis of lectin-sugar interactions in the complexes shows that they are more extensive when the beta-anomer is involved in the linkage. As expected, the second sugar residue is ill-defined when the linkage is 1-->6. There are more than two dozen water molecules which occur in the hydration shells of all structures determined at resolutions better than 2.5 A. Most of them are involved in stabilizing the structure, particularly loops. Water molecules involved in lectin-sugar interactions are also substantially conserved. The lectin molecule is fairly rigid and does not appear to be affected by changes in temperature.

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“…Analyses were performed with various tools available in the GROMACS suite and self‐written programs and scripts. Internet server PDB Goodies41 has been used at various stages of the study. Figures have been prepared using PyMOL (http://www.pymol.org).…”

Section: Methodsmentioning

confidence: 99%

Structure, dynamics, and interactions of jacalin. Insights from molecular dynamics simulations examined in conjunction with results of X‐ray studies

Sharma

Sekar²,

Vijayan

2009

Proteins

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Molecular dynamics simulations have been carried out on all the jacalin-carbohydrate complexes of known structure, models of unliganded molecules derived from the complexes and also models of relevant complexes where X-ray structures are not available. Results of the simulations and the available crystal structures involving jacalin permit delineation of the relatively rigid and flexible regions of the molecule and the dynamical variability of the hydrogen bonds involved in stabilizing the structure. Local flexibility appears to be related to solvent accessibility. Hydrogen bonds involving side chains and water bridges involving buried water molecules appear to be important in the stabilization of loop structures. The lectin-carbohydrate interactions observed in crystal structures, the average parameters pertaining to them derived from simulations, energetic contribution of the stacking residue estimated from quantum mechanical calculations, and the scatter of the locations of carbohydrate and carbohydrate-binding residues are consistent with the known thermodynamic parameters of jacalin-carbohydrate interactions. The simulations, along with X-ray results, provide a fuller picture of carbohydrate binding by jacalin than provided by crystallographic analysis alone. The simulations confirm that in the unliganded structures water molecules tend to occupy the positions occupied by carbohydrate oxygens in the lectin-carbohydrate complexes. Population distributions in simulations of the free lectin, the ligands, and the complexes indicate a combination of conformational selection and induced fit.

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PDB Goodies – a web-based GUI to manipulate the Protein Data Bank file

Cited by 27 publications

References 2 publications

Structure of SAICAR synthetase from Pyrococcus horikoshii OT3: Insights into thermal stability

Structure of SAICAR synthetase from Pyrococcus horikoshii OT3: Insights into thermal stability

Structural studies on peanut lectin complexed with disaccharides involving different linkages: further insights into the structure and interactions of the lectin

Structure, dynamics, and interactions of jacalin. Insights from molecular dynamics simulations examined in conjunction with results of X‐ray studies

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