PortoBioComp

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…

mm:parameters:iron:cc_c_2

2013-10-03T18:59:50+01:00

Desulforedoxin is a mononuclear iron tetrahedral metal center coordinated with two directly linked cysteines and and two cysteines that are not linked. COORDINATION SPHERE Oxidation State: Fe(III) Spin Multiplicity: 6 ---------- Structure chosen to parameterize TEST PROTEIN Protein Desulforedoxin PDB Code 1DXG Crystallographic Resolution 1.80 Å Organism Desulfovibrio gigas [Archer, 1995] Parameters Determined Atom Types ATOM TYPE NEW ATOM TYPE …

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: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:manganese:hhdhwa

2013-10-03T18:57:04+01:00

The coordination sphere of Manganese Superoxide Dismutase is located in a hydrophobic pocket formed by two subunits. In the resting state the manganese coordination geometry presents distorted trigonal bipyramidal geometry with two histidine and an aspartate equatorial ligands and a histidine and water/hydroxide in axial positions. COORDINATION SPHERE Oxidation State: Mn(III) Spin Multiplicity: 5

mm:parameters:manganese:hhdh_ho

2013-10-03T18:55:50+01:00

mm:parameters:manganese:hdewawawa

2013-10-03T18:54:49+01:00

In Citochrome c Oxidase the manganese ion has a nonredox role. Manganese(II) is bonded to residues from different subunits: a glutamate, an aspartate and histidine ligands and possibly one to three water molecules. The glutamate ligand is also coordinated to a copper atom and the histidine is hydrogen bonded to a heme a3 propionate. COORDINATION SPHERE Oxidation State: Mn(II) Spin Multiplicity: 6

compasm

2013-10-03T09:53:05+01:00

Operating systems: Windows, MacOS and Linux. Contacts : João Ribeiro Nuno Sousa Cerqueira Pedro A. Fernandes Maria João Ramos ---------- Citation : CompASM: an Amber-VMD alanine scanning mutagenesis plug-in. J. Ribeiro, N. M. F. S. A. Cerqueira, I. S. Moreira, P. A. Fernandes AND M. J. Ramos Theoretical Chemistry Accounts, 2012, 131:1271 10.1007/s00214-012-1271-2

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