PortoBioComp

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.

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

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…

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

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

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

sidebar

2017-06-19T13:25:45+01:00

Home Research Data * Benchmarks * Molecular Mechanics Parameters * Enzymatic Mechanisms Software * VsLab * MADAMM * VolArea * compASM * VMDMagazine * Chem-Path-Tracker * Selection Manager * molUP * Scripts

selection_manager

2014-04-25T14:04:32+01:00

Operating systems: MacOS and Linux. Contacts : Nuno Sousa Cerqueira ---------- 1. Introduction VMD is an exceptional program to visualize molecular structures. The main drawback of this software is the learning curve that turns it hard to use by non-expert users. One of the major difficulties that non-expert users have while handling VMD regards the selection of atoms. This is done through a series of keywords that the user must dominate in order to for example visualize and/or hide parti…

selector_manager

2014-03-11T11:35:27+01:00

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 …

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

frontpage

2017-06-19T14:15:17+01:00

In an Era in which science is globalized, now more than ever, we feel it is necessary to make our lines of work available for any investigator, in and out of our field of work.This website is therefore built to divulge the Theoretical Chemistry and Computational Biochemistry Group, established in the Faculty of Sciences, University of Porto.

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: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: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: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: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: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: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

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: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: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

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: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

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…

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…

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: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…