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…

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:lipids

2013-10-03T18:59:55+01:00

[ ] Phosphatidylcholines (PC) Phosphatidylethanolamines (PE) The following charge parameters for 12 distinct phospholipids were determined, following an AMBER compatible approach. These parameters were validated by building a bilayer system for each phospholipid type and by comparing structural and dynamical values with experimental available data. When considering the DOPC phospholipid a good correlation with experimental available data was obtained. These parameters were obtained under…

mm:parameters:lipids:example_page

2013-07-25T19:24:42+01:00

The following charge parameters for 12 distinct phospholipids were determined, following an AMBER compatible approach. These parameters were validated by building a bilayer system for each phospholipid type and by comparing structural and dynamical values with experimental data available. Some validation results are displayed at the end of the page, and for the DOPC phospholipid a good correlation with experimental available data was obtained.

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.

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

wiki:syntax

2013-05-10T13:45:54+01:00

DokuWiki supports some simple markup language, which tries to make the datafiles to be as readable as possible. This page contains all possible syntax you may use when editing the pages. Simply have a look at the source of this page by pressing “Edit this page”. If you want to try something, just use the playground page. The simpler markup is easily accessible via quickbuttons, too.

scripts

2013-10-02T14:28:14+01:00

The scripts available on this page were developed in our research group.

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: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…

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, …

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.

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…

wiki:dokuwiki

2013-05-10T13:45:54+01:00

DokuWiki is a standards compliant, simple to use Wiki, mainly aimed at creating documentation of any kind. It is targeted at developer teams, workgroups and small companies. It has a simple but powerful syntax which makes sure the datafiles remain readable outside the Wiki and eases the creation of structured texts. All data is stored in plain text files -- no database is required.

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.

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…

wiki:welcome

2013-05-10T13:45:54+01:00

Congratulations, your wiki is now up and running. Here are a few more tips to get you started. Enjoy your work with DokuWiki, -- the developers Create your first pages Your wiki needs to have a start page. As long as it doesn't exist, this link will be red: start.