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

chem-path-tracker

2014-02-05T16:36:53+01:00

Operating systems: Windows, MacOS and Linux. Contacts : João Ribeiro Nuno Sousa Cerqueira Pedro A. Fernandes Maria João Ramos ---------- 1. Introduction Chem-Path-Tracker is a bioinformatic tool that allows to locate functionally relevant chemical motifs in protein structures.The chemical motifs can be a small group of residues or structure protein fragments with highly conserved properties that have important biological functions. However, the detection of chemical motifs is rather diffic…

biopathfinder

2013-10-09T17:17:19+01:00

Operating systems: Windows, MacOS and Linux. Contacts : João Ribeiro Nuno Sousa Cerqueira Pedro A. Fernandes Maria João Ramos ---------- 1. Introduction BioPathFinder is a bioinformatic tool that allows to locate functionally relevant chemical motifs in protein structures.The chemical motifs can be a small group of residues or structure protein fragments with highly conserved properties that have important biological functions. However, the detection of chemical motifs is rather difficult …

madamm

2013-10-03T09:56:41+01:00

Operating systems: MacOS and Linux. Contacts : Nuno Sousa Cerqueira Pedro A. Fernandes Maria João Ramos ---------- Citation : MADAMM: a multistaged docking with an automated molecular modeling protocol. N. M. F. S. A. Cerqueira, N. F. Bras, P. A. Fernandes AND M. J. Ramos Proteins (Structure, Function, Bioinformatics), 2009, 74(1):192–206 DOI:10.1002/prot.22146

mm:parameters:iron:cccc

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

Rubredoxin is a mononuclear iron tetrahedral metal center coordinated with four cysteines that are not directly connected in the backbone of the protein. COORDINATION SPHERE Oxidation State: Fe(III) Spin Multiplicity: 6 ---------- Structure chosen to parameterize TEST PROTEIN Protein Rubredoxin PDB Code 1IRO Crystallographic Resolution 1.10 Å Organism Clostridium pasteurianum [Dauter, 1996] Parameters Determined Atom Types ATOM TYPE NEW ATOM TY…

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:manganese:dedwawawa

2013-10-03T18:51:33+01:00

Muconate Cycloisomerase shows preference on manganese(II) over the magnesium ion to perform. Its coordination sphere is similar to the one found in chloromuconate cycloisomerase, with two aspartates and a glutamate. COORDINATION SPHERE Oxidation State: Mn(II) Spin Multiplicity: 6

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

mm:parameters:manganese:denwawawa

2013-10-03T18:53:33+01:00

D-Glutarate Dehydratase is analogous to mandelate racemase and enolase. The manganese coordination sphere has a manganese(II) atom bonded to a glutamate, an aspartate and an asparagine from the same subunit. COORDINATION SPHERE Oxidation State: Mn(II) Spin Multiplicity: 6

mm:parameters:manganese:dee_so2

2013-10-03T18:52:37+01:00

Crystal structures from Mandelate Racemase show that it is octameric. The manganese(II) atom in this enzyme is bonded to the side chains of an aspartate, two glutamates and it is bidentate either to a sulfate ion or a S-altrolactate. COORDINATION SPHERE Oxidation State: Mn(II) Spin Multiplicity: 6

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

mm:parameters:manganese:ded_cl

2013-10-03T18:50:44+01:00

The metal atom of Chloromuconate Cycloisomerase is shown to be bonded to two aspartates, a glutamate and chloride ion. COORDINATION SPHERE Oxidation State: Mn(II) Spin Multiplicity: 6 ---------- Structure chosen to parameterize TEST PROTEIN Protein Chloromuconate Cycloisomerase PDB Code 2CHR Crystallographic Resolution 3.00 Å Organism Cupriavidus necator [Kleywegt, 1996] Parameters Determined Atom Types ATOM TYPE NEW ATOM TYPE MASS STRUCTU…

mm:parameters:manganese:ed_py2_wawa

2013-10-03T18:55:04+01:00

In Pyruvate Kinase manganese(II) mediates the allosteric communication between the phosphoenolpyruvate and fructose-1,6-bisphosphate. Crystal structures suggest that manganese(II) bonds to aspartate, glutamate and the oxygen from a carbonyl and carboxylate groups from a pyruvate ligand. A water molecule is referred as participating in the octahedral coordination of manganese(II). 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:manganese:ddwawawawa

2013-10-03T18:46:30+01:00

The avian viral S integrase shows preference by manganese(II) over magnesium. In both cases the metal atom is bonded to two aspartates and four water molecules. COORDINATION SPHERE Oxidation state: Mn(II) Spin multiplicity: 6 ---------- Structure chosen to parameterize TEST PROTEIN Protein Integrase PDB Code 1A5V Crystallographic Resolution 1.90 Å Organism Rous Sarcoma Virus [Lubkowski, 1998] Parameters Determined Atom Types ATOM TYPE NEW ATOM …

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:manganese:hhdh_ho

2013-10-03T18:55:50+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:hhdhwa

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

mm:parameters:manganese:hhe_d2

2013-10-03T18:57:45+01:00

During the crystallographic refinements of Pneumococcal Surface Antigen Adhesin A the metal ion was modeled as zinc, with attempts to model manganese(II) failed. The metal atom is expected to be tetrahedral bonded to two histidines, a glutamate and an aspartate, with angles ranging from 93o to 131o. COORDINATION SPHERE Oxidation State: Mn(II) Spin Multiplicity: 6

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: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:manganese:hhewawa

2013-10-03T18:58:24+01:00

Homoprotocatechuate-2,3-deoxygenase is shown to have five ligands bonded to the iron(II) ion: a glutamate, two histidines and two waters in a square pyramidal geometry. The ligands in manganese(II) deoxygenases are likely to be the same. Other studies show, however, that it might be hexacoordinated with three solvent molecules occupying ligand positions. COORDINATION SPHERE Oxidation State: Mn(II) Spin Multiplicity: 5

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: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:iron:cc_fe_ss_fe_cc

2013-10-03T19:00:23+01:00

Ferredoxin is a binuclear iron center with four cysteine residues and two sulfurs, having a redox potential of 400 mV. COORDINATION SPHERE Oxidation State: Fe(III)/Fe(III) Spin Multiplicity: 1 ---------- Structure chosen to parameterize TEST PROTEIN Protein [2Fe-2S] Ferredoxin PDB Code 4FXC Crystallographic Resolution 2.50 Å Organism Spirulina platensis [Fukuyama, 1995] Parameters Determined Atom Types ATOM TYPE NEW ATOM TYPE MASS STRUC…

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)

mm:parameters:copper

2013-08-06T15:57:39+01:00

INDEX BY METALLOCENTRE [ ] HHH[Cu]H[Zn]DHH ---------- INDEX BY PROTEIN Cu, Zn Superoxide Dismutase

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.

mm:parameters:iron

2013-08-06T14:52:21+01:00

[ ] CCCC CC[C]2 CC[FE]SS[FE]CC ---------- INDEX BY PROTEIN Rubredoxin Desulforedoxin Ferrodoxin

mm:parameters:manganese

2013-08-05T19:18:59+01:00

INDEX BY METALLOCENTRE [ ] DDWaWaWaWa DED[CL] DEDWaWaWa DEE[SO2] DENWaWaWa ED[PY2]WaWa HDEWaWaWa HHDH[HO] HHDH[HO]O HHDHWa HHE[D2] HHEWaWa ---------- INDEX BY PROTEIN Superoxide Dismutase (resting state) Superoxide Dismutase (resting state) Superoxide Dismutase (with substrate) Citochrome C Oxidase D-Glutarate Dehydratase Integrase Muconate Cycloisomerase Pyruvate Kinase Homoprotocatechuate-2,3-Dioxygenase Mandelate…

molup

2018-10-11T17:17:59+01:00

Operating systems: macOS, Linux, and Windows (NEW) Contacts : Henrique Silva Fernandes Maria João Ramos Nuno Sousa Cerqueira ---------- 1. Introduction molUP is a VMD extension that provides a simple manner for loading and saving Gaussian files, and analyze related results. molUP provides a graphical interface for VMD where the users can load and save chemical structures in the Gaussian file formats. This extension includes a set of tools to set up any calculation supported by Gaussian, …