PortoBioComp

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: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: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

vmdmagazine

2017-06-30T15:00:30+01:00

Operating systems: Windows, MacOS and Linux. Contacts : Nuno Sousa Cerqueira Pedro A. Fernandes Maria João Ramos ---------- 1. Introduction Visualization can be a motivating way of teaching students about the microscopic world. This can become even more exciting if the information is based on accurate computational results rather than on crude approximations that eventually might create unreal alternative perceptions. Here, we report on a VMD plug-in – VMDMagazine, which can play and…

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…

software

2017-06-30T11:26:12+01:00

List of Software currently available on the PortoBioComp Database: ---------- VsLab - VMD plug-in vsLab (Virtual Screening LABoratory) is an easy-to-use graphical interface for the well known molecular docking software AutoGrid/AutoDock that has been included into VMD as a plug-in. This program allows almost anyone to use AutoDock and AutoGrid for simple docking or for virtual screening campaigns without requiring any deep knowledge about these techniques.

benchmarks

2017-06-12T16:16:44+01:00

Contents : Several Density Functional Theory (DFT) benchmarks have been performed by our group. DFT is less demanding than other computational methods with similar accuracy; and is able to include electron correlation in the calculations at a fraction of the time of post-Hartree-Fock methodologies. It also permits the study of molecular systems containing up to 200 atoms, a feature that is not yet feasible with high accuracy methods such as CCSD(T) or even secondord…

vslab

2014-03-10T15:18:41+01:00

Operating systems: MacOS and Linux. Contacts : Nuno Sousa Cerqueira Pedro A. Fernandes Maria João Ramos ---------- Citation : VsLab—An implementation for virtual high-throughput screening using AutoDock and VMD. N. M. F. S. A. Cerqueira, J. Ribeiro, P. A. Fernandes AND M. J. Ramos International Journal of Quantum Chemistry, 2011, 111(6):1208–1212 DOI:10.1002/qua.22738

mm:parameters:manganese:hhdh_ho_o

2013-10-03T18:56:25+01:00

Electronic spectroscopy studies on the resting and enzyme-substrates states of Manganese Superoxide Dismutase support the hypothesis of a side-on peroxo complex with the superoxide anion. The superoxide anion coordinates to the manganese ion between two histidines. The spin multiplicity of the coordination sphere has been reported as a quartet, due to an antiferromagnetic coupling between the superoxide and manganese species. COORDINATION SPHERE Oxidation State: Mn(III) Spin Multiplic…

mm:parameters:zinc

2013-08-06T15:56:22+01:00

INDEX BY METALLOCENTRE [ ] HC[D2] HDCC HDC[CZL] HHH[Cu]H[Zn]DHH ---------- INDEX BY PROTEIN Farnesyltransferase (resting state) Farnesyltransferase (with FPP) Farnesyltransferase (with farnesyl diphosphate and peptide inhibitor) Farnesyltransferase (with product)