The Experts below are selected from a list of 60774 Experts worldwide ranked by ideXlab platform
Isabel C F R Ferreira - One of the best experts on this subject based on the ideXlab platform.
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mola a bootable self configuring system for virtual screening using autodock4 vina on computer clusters
Journal of Cheminformatics, 2010Co-Authors: Rui M V Abreu, Hugo J C Froufe, Maria Joao R P Queiroz, Isabel C F R FerreiraAbstract:Virtual screening of small molecules using molecular docking has become an important Tool in drug discovery. However, large scale virtual screening is time demanding and usually requires dedicated computer clusters. There are a number of software Tools that perform virtual screening using AutoDock4 but they require access to dedicated Linux computer clusters. Also no software is available for performing virtual screening with Vina using computer clusters. In this paper we present MOLA, an easy-to-use graphical User Interface Tool that automates parallel virtual screening using AutoDock4 and/or Vina in bootable non-dedicated computer clusters. MOLA automates several tasks including: ligand preparation, parallel AutoDock4/Vina jobs distribution and result analysis. When the virtual screening project finishes, an open-office spreadsheet file opens with the ligands ranked by binding energy and distance to the active site. All results files can automatically be recorded on an USB-flash drive or on the hard-disk drive using VirtualBox. MOLA works inside a customized Live CD GNU/Linux operating system, developed by us, that bypass the original operating system installed on the computers used in the cluster. This operating system boots from a CD on the master node and then clusters other computers as slave nodes via ethernet connections. MOLA is an ideal virtual screening Tool for non-experienced Users, with a limited number of multi-platform heterogeneous computers available and no access to dedicated Linux computer clusters. When a virtual screening project finishes, the computers can just be restarted to their original operating system. The originality of MOLA lies on the fact that, any platform-independent computer available can he added to the cluster, without ever using the computer hard-disk drive and without interfering with the installed operating system. With a cluster of 10 processors, and a potential maximum speed-up of 10x, the parallel algorithm of MOLA performed with a speed-up of 8,64× using AutoDock4 and 8,60× using Vina.
Tsukasa Kawaoka - One of the best experts on this subject based on the ideXlab platform.
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Interfacer a User Interface Tool for interactive expert systems
Decision Support Systems, 1996Co-Authors: Shigeo Kaneda, Megumi Ishii, Fumio Hattori, Tsukasa KawaokaAbstract:Abstract From the User Interface point of view, expert-systems are different from conventional applications in some features. First, the User query sequence highly depends upon input data up to that time. Second, any change in query sequence requires highly complicated data modification routines. Thus, User Interface implementation is a bottleneck in the same manner as knowledge acquisition is the bottleneck for expert-systems. To resolve this problem, this paper proposes the User Interface Tool “InterfaceR” for interactive expert-systems. InterfaceR automatically generates a User Interface screen according to the data input query requirement from the inference engine, and requires no User data modification routines in expert-system development. We applied the proposed InterfaceR to a practical middle-scale business system: The General Employee Affairs Expert-system. Program amount was decreased 50% compared to the conventional procedural implementation.
Rui M V Abreu - One of the best experts on this subject based on the ideXlab platform.
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mola a bootable self configuring system for virtual screening using autodock4 vina on computer clusters
Journal of Cheminformatics, 2010Co-Authors: Rui M V Abreu, Hugo J C Froufe, Maria Joao R P Queiroz, Isabel C F R FerreiraAbstract:Virtual screening of small molecules using molecular docking has become an important Tool in drug discovery. However, large scale virtual screening is time demanding and usually requires dedicated computer clusters. There are a number of software Tools that perform virtual screening using AutoDock4 but they require access to dedicated Linux computer clusters. Also no software is available for performing virtual screening with Vina using computer clusters. In this paper we present MOLA, an easy-to-use graphical User Interface Tool that automates parallel virtual screening using AutoDock4 and/or Vina in bootable non-dedicated computer clusters. MOLA automates several tasks including: ligand preparation, parallel AutoDock4/Vina jobs distribution and result analysis. When the virtual screening project finishes, an open-office spreadsheet file opens with the ligands ranked by binding energy and distance to the active site. All results files can automatically be recorded on an USB-flash drive or on the hard-disk drive using VirtualBox. MOLA works inside a customized Live CD GNU/Linux operating system, developed by us, that bypass the original operating system installed on the computers used in the cluster. This operating system boots from a CD on the master node and then clusters other computers as slave nodes via ethernet connections. MOLA is an ideal virtual screening Tool for non-experienced Users, with a limited number of multi-platform heterogeneous computers available and no access to dedicated Linux computer clusters. When a virtual screening project finishes, the computers can just be restarted to their original operating system. The originality of MOLA lies on the fact that, any platform-independent computer available can he added to the cluster, without ever using the computer hard-disk drive and without interfering with the installed operating system. With a cluster of 10 processors, and a potential maximum speed-up of 10x, the parallel algorithm of MOLA performed with a speed-up of 8,64× using AutoDock4 and 8,60× using Vina.
Shigeo Kaneda - One of the best experts on this subject based on the ideXlab platform.
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Interfacer a User Interface Tool for interactive expert systems
Decision Support Systems, 1996Co-Authors: Shigeo Kaneda, Megumi Ishii, Fumio Hattori, Tsukasa KawaokaAbstract:Abstract From the User Interface point of view, expert-systems are different from conventional applications in some features. First, the User query sequence highly depends upon input data up to that time. Second, any change in query sequence requires highly complicated data modification routines. Thus, User Interface implementation is a bottleneck in the same manner as knowledge acquisition is the bottleneck for expert-systems. To resolve this problem, this paper proposes the User Interface Tool “InterfaceR” for interactive expert-systems. InterfaceR automatically generates a User Interface screen according to the data input query requirement from the inference engine, and requires no User data modification routines in expert-system development. We applied the proposed InterfaceR to a practical middle-scale business system: The General Employee Affairs Expert-system. Program amount was decreased 50% compared to the conventional procedural implementation.
Maria Joao R P Queiroz - One of the best experts on this subject based on the ideXlab platform.
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mola a bootable self configuring system for virtual screening using autodock4 vina on computer clusters
Journal of Cheminformatics, 2010Co-Authors: Rui M V Abreu, Hugo J C Froufe, Maria Joao R P Queiroz, Isabel C F R FerreiraAbstract:Virtual screening of small molecules using molecular docking has become an important Tool in drug discovery. However, large scale virtual screening is time demanding and usually requires dedicated computer clusters. There are a number of software Tools that perform virtual screening using AutoDock4 but they require access to dedicated Linux computer clusters. Also no software is available for performing virtual screening with Vina using computer clusters. In this paper we present MOLA, an easy-to-use graphical User Interface Tool that automates parallel virtual screening using AutoDock4 and/or Vina in bootable non-dedicated computer clusters. MOLA automates several tasks including: ligand preparation, parallel AutoDock4/Vina jobs distribution and result analysis. When the virtual screening project finishes, an open-office spreadsheet file opens with the ligands ranked by binding energy and distance to the active site. All results files can automatically be recorded on an USB-flash drive or on the hard-disk drive using VirtualBox. MOLA works inside a customized Live CD GNU/Linux operating system, developed by us, that bypass the original operating system installed on the computers used in the cluster. This operating system boots from a CD on the master node and then clusters other computers as slave nodes via ethernet connections. MOLA is an ideal virtual screening Tool for non-experienced Users, with a limited number of multi-platform heterogeneous computers available and no access to dedicated Linux computer clusters. When a virtual screening project finishes, the computers can just be restarted to their original operating system. The originality of MOLA lies on the fact that, any platform-independent computer available can he added to the cluster, without ever using the computer hard-disk drive and without interfering with the installed operating system. With a cluster of 10 processors, and a potential maximum speed-up of 10x, the parallel algorithm of MOLA performed with a speed-up of 8,64× using AutoDock4 and 8,60× using Vina.
