https://www.fc.up.pt/PortoBioComp/database/ 2026-05-06T09:52:13+01:00 https://www.fc.up.pt/PortoBioComp/database/ https://www.fc.up.pt/PortoBioComp/database/lib/tpl/dokuwiki/images/favicon.ico text/html 2018-10-11T17:17:59+01:00 https://www.fc.up.pt/PortoBioComp/database/doku.php?id=molup&rev=1539274679&do=diff 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, … text/html 2017-06-30T15:00:30+01:00 https://www.fc.up.pt/PortoBioComp/database/doku.php?id=vmdmagazine&rev=1498831230&do=diff 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… text/html 2017-06-12T16:16:44+01:00 https://www.fc.up.pt/PortoBioComp/database/doku.php?id=benchmarks&rev=1497280604&do=diff Contents : <!-- INLINETOCPLACEHOLDER --> 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… text/html 2014-06-30T11:26:35+01:00 https://www.fc.up.pt/PortoBioComp/database/doku.php?id=volarea&rev=1404123995&do=diff 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 text/html 2014-04-25T14:04:32+01:00 https://www.fc.up.pt/PortoBioComp/database/doku.php?id=selection_manager&rev=1398431072&do=diff 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… text/html 2014-03-11T11:35:27+01:00 https://www.fc.up.pt/PortoBioComp/database/doku.php?id=selector_manager&rev=1394537727&do=diff 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… text/html 2014-03-10T15:18:41+01:00 https://www.fc.up.pt/PortoBioComp/database/doku.php?id=vslab&rev=1394464721&do=diff 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 text/html 2014-02-05T16:36:53+01:00 https://www.fc.up.pt/PortoBioComp/database/doku.php?id=chem-path-tracker&rev=1391618213&do=diff 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… text/html 2013-10-09T17:17:19+01:00 https://www.fc.up.pt/PortoBioComp/database/doku.php?id=biopathfinder&rev=1381335439&do=diff 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 … text/html 2013-10-03T19:02:30+01:00 https://www.fc.up.pt/PortoBioComp/database/doku.php?id=molecular_mechanics&rev=1380823350&do=diff ---------- 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… text/html 2013-10-03T09:56:41+01:00 https://www.fc.up.pt/PortoBioComp/database/doku.php?id=madamm&rev=1380790601&do=diff 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 text/html 2013-10-03T09:53:05+01:00 https://www.fc.up.pt/PortoBioComp/database/doku.php?id=compasm&rev=1380790385&do=diff 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