https://web.fc.up.pt/PortoBioComp/database/ 2026-05-06T15:36:26+01:00 https://web.fc.up.pt/PortoBioComp/database/ https://web.fc.up.pt/PortoBioComp/database/lib/tpl/dokuwiki/images/favicon.ico text/html 2014-03-10T15:18:41+01:00 https://web.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 2017-06-30T15:00:30+01:00 https://web.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 2017-06-19T14:15:17+01:00 https://web.fc.up.pt/PortoBioComp/database/doku.php?id=frontpage&rev=1497878117&do=diff 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. text/html 2013-10-03T09:56:41+01:00 https://web.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 2017-06-19T13:25:45+01:00 https://web.fc.up.pt/PortoBioComp/database/doku.php?id=sidebar&rev=1497875145&do=diff Home Research Data * Benchmarks * Molecular Mechanics Parameters * Enzymatic Mechanisms Software * VsLab * MADAMM * VolArea * compASM * VMDMagazine * Chem-Path-Tracker * Selection Manager * molUP * Scripts text/html 2014-06-30T11:26:35+01:00 https://web.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://web.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://web.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 2014-02-05T16:36:53+01:00 https://web.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://web.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 2013-10-03T09:53:05+01:00 https://web.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 text/html 2013-10-02T14:28:14+01:00 https://web.fc.up.pt/PortoBioComp/database/doku.php?id=scripts&rev=1380720494&do=diff The scripts available on this page were developed in our research group.