PortoBioComp

vmdmagazinedatabase

2017-06-30T11:58:38+01:00

Contents : Note: All the data present in this database are derived from theoretical and computational calculations or obtained from experimental sources. ---------- Allotropy is the property of some chemical elements to exist in two or more different forms, known as allotropes of these elements. Allotropes of the same element can exhibit quite different physical properties and chemical behaviours.Allotropes of carbon include diamond (where the carbon atoms are bon…

volarea

2014-06-30T11:26:35+01:00

Operating systems: Windows, MacOS and Linux. Contacts : João Ribeiro Nuno Sousa Cerqueira Pedro A. Fernandes Maria João Ramos ---------- Citation : A VMD Plug-in to measure the Surface and calculate the Volume of proteins. J. Ribeiro, N. M. F. S. A. Cerqueira, , P. A. Fernandes AND M. J. Ramos Chemical Biology & Drug Design, 2013, in press

molecular_mechanics

2013-10-03T19:02:30+01:00

---------- The AMBER family of force fields is one of the most commonly used alternatives to describe proteins and drug-like molecules in molecular dynamics simulations. The Data Base presented comprehends sets of parameters developed by the group during round the last ten years. * A first set of parameters accounts for the systematic parameterization of 12 common lipid types consistent with the General Amber Force Field (GAFF), with charge-parameters determined with RESP at the HF/6–31G(d) le…

mm:parameters:lipids:phosphatidylethanolamines_pe

2013-10-03T19:00:42+01:00

For each phospholipid, its name, 4-letter code, composition of aliphatic chains (sn1/sn2), and parameter files are presented. In addition, the values for volume per lipid (VL), area per lipid (AL), and bilayer thickness (DHH) in a bilayer setting are given, together with experimental data (when available). These parameters were obtained under the General Amber Force Field (GAFF) terminology and general parameters.

mm:parameters:lipids:phosphatidylcholines_pc

2013-10-03T19:00:15+01:00

For each phospholipid, its name, 4-letter code, composition of aliphatic chains (sn1/sn2), and parameter files are presented. In addition, the values for volume per lipid (VL), area per lipid (AL), and bilayer thickness (DHH) in a bilayer setting are given, together with experimental data (when available). For the DOPC phospholipid, order parameters for the acyl chains are displayed and compared with experiment. These parameters were obtained under the General Amber Force Field (GAFF) terminolog…

mm:parameters:zinc:hdc_czl

2013-10-03T18:59:21+01:00

The metal center of Farnesyltransferase for the product complex is hereby presented, in which the Zinc atom is bonded to 1 histidine, 1 cysteine, 1 aspartate (monodentate), and to the product (CZL). COORDINATION SPHERE Oxidation state: Zn(II) Spin multiplicity: 1

mm:parameters:copper_zinc:hhh_cu_h_zn_dhh

2013-10-03T18:58:39+01:00

The metal center of Cu, Zn Superoxide Dismutase is hereby presented, in which the zinc atom is bonded to 3 histidines, and 1 aspartate (monodentate) and the copper atom to 4 histidines. Validation for this metal centre in the protein environment is additionally provided. COORDINATION SPHERE Oxidation state: Cu(II) / Zn(II) Spin multiplicity: 1

mm:parameters:zinc:hc_d2

2013-10-03T18:58:12+01:00

The metal center of Farnesyltransferase in the resting state is hereby presented, in which the Zinc atom is bonded to 1 histidine, 1 cysteine and to 1 aspartate (bidentate). Validation for the binary complex is additionally provided. COORDINATION SPHERE Oxidation state: Zn(II) Spin multiplicity: 1

mm:parameters:zinc:hdcc

2013-10-03T18:57:53+01:00

The metal center of Farnesyltransferase for the ternary complex is hereby presented, in which the Zinc atom is bonded to 1 histidine, 2 cysteine residues (1 from the peptide inhibitor) and to 1 aspartate (monodentate). COORDINATION SPHERE Oxidation state: Zn(II) Spin multiplicity: 1

mm:parameters:zinc:hdc

2013-08-06T15:33:59+01:00

The metal center of Farnesyltransferase in the resting state is hereby presented, in which the Zinc atom is bonded to 1 histidine, 1 cysteine and to 1 aspartate (bidentate). Validation for the binary complex is additionally provided. Coordination Sphere Oxidation state: Zn(II) Spin multiplicity: 1 JMOL

mm:parameters:zinc:hdc_fp

2013-08-05T14:53:46+01:00

The metal center of Farnesyltransferase for the product complex is hereby presented, in which the Zinc atom is bonded to 1 histidine, 1 cysteine, 1 aspartate (monodentate), and to the product. Coordination Sphere Oxidation state: Zn(II) Spin multiplicity: 1