Jose Garzon - Academia.edu (original) (raw)
Papers by Jose Garzon
... Para las áreas metropolitanas tenemos que la zona que mayor producción bruta tiene es la de B... more ... Para las áreas metropolitanas tenemos que la zona que mayor producción bruta tiene es la de Bogota DC - Soacha, con un 28.9% luego se ubica el área de Medellín – Valle de Aburrá, queparticipa con un 23.1%. Pos-teriormente, la zona de Cali-Yumbo con un 22.8%. ...
Food Policy, 1984
This article reviews the experience of the US Food for Peace Program (PL 480) under Title III, wi... more This article reviews the experience of the US Food for Peace Program (PL 480) under Title III, with the objective of identifying some of the limitations and possibilities of using food aid as a development tool. It will argue that while multi-year agreements are inflexible, the settings in which the agreements are to be implemented are turbulent and uncertain. Combining food aid with development also makes severe demands upon the administrative capacity of both field missions and recipients, resulting in a reluctance on the part of both to initiate agreements.
International Journal of Urban and Regional Research, 1985
Food Policy, 1984
This article reviews the experience of the US Food for Peace Program (PL 480) under Title III, wi... more This article reviews the experience of the US Food for Peace Program (PL 480) under Title III, with the objective of identifying some of the limitations and possibilities of using food aid as a development tool. It will argue that while multi-year agreements are inflexible, the settings in which the agreements are to be implemented are turbulent and uncertain. Combining food aid with development also makes severe demands upon the administrative capacity of both field missions and recipients, resulting in a reluctance on the part of both to initiate agreements.
2014 22nd Euromicro International Conference on Parallel, Distributed, and Network-Based Processing, 2014
The procedure for screening large databases of small chemical compounds to select likely drug can... more The procedure for screening large databases of small chemical compounds to select likely drug candidates by computational means is very time demanding. Here, we present and evaluate a new method for virtual screening (VS) that combines the efficiency of spherical harmonic approximations to accelerate the rotational part of a docking search with multicore and GPU parallelism. To validate these novel parallel algorithms, we used standard benchmark cases. The obtained results are comparable to those generated via state-of-the-art VS docking approximations, but with a considerable gain in efficiency. GPU implementation speedups of more than 30-fold with respect to a single core CPU were achieved, reducing the docking time for a single ligand to only 50 milliseconds. The achieved efficiency and the accuracy on standard blind benchmarks demonstrate the applicability and robustness of this approach.
Bioinformatics/computer Applications in The Biosciences, 2009
Prediction of protein-protein complexes from the coordinates of their unbound components usually ... more Prediction of protein-protein complexes from the coordinates of their unbound components usually starts by generating many potential predictions from a rigid-body 6D search followed by a second stage that aims to refine such predictions. Here, we present and evaluate a new method to effectively address the complexity and sampling requirements of the initial exhaustive search. In this approach we combine the projection of the interaction terms into 3D grid-based potentials with the efficiency of spherical harmonics approximations to accelerate the search. The binding energy upon complex formation is approximated as a correlation function composed of van der Waals, electrostatics and desolvation potential terms. The interaction-energy minima are identified by a novel, fast and exhaustive rotational docking search combined with a simple translational scanning. Results obtained on standard protein-protein benchmarks demonstrate its general applicability and robustness. The accuracy is comparable to that of existing stateof-the-art initial exhaustive rigid-body docking tools, but achieving superior efficiency. Moreover, a parallel version of the method performs the docking search in just a few minutes, opening new application opportunities in the current 'omics' world.
PLoS ONE, 2014
The distance-dependent knowledge-based DrugScore(PPI) potentials, previously developed for in sil... more The distance-dependent knowledge-based DrugScore(PPI) potentials, previously developed for in silico alanine scanning and hot spot prediction on given structures of protein-protein complexes, are evaluated as a scoring and objective function for the structure prediction of protein-protein complexes. When applied for ranking "unbound perturbation" ("unbound docking") decoys generated by Baker and coworkers a 4-fold (1.5-fold) enrichment of acceptable docking solutions in the top ranks compared to a random selection is found. When applied as an objective function in FRODOCK for bound protein-protein docking on 97 complexes of the ZDOCK benchmark 3.0, DrugScore(PPI)/FRODOCK finds up to 10% (15%) more high accuracy solutions in the top 1 (top 10) predictions than the original FRODOCK implementation. When used as an objective function for global unbound protein-protein docking, fair docking success rates are obtained, which improve by ∼ 2-fold to 18% (58%) for an at least acceptable solution in the top 10 (top 100) predictions when performing knowledge-driven unbound docking. This suggests that DrugScore(PPI) balances well several different types of interactions important for protein-protein recognition. The results are discussed in view of the influence of crystal packing and the type of protein-protein complex docked. Finally, a simple criterion is provided with which to estimate a priori if unbound docking with DrugScore(PPI)/FRODOCK will be successful.
Journal of Software, 2007
Rigid body fitting is the common way to interpret the 3D information contained in a electron micr... more Rigid body fitting is the common way to interpret the 3D information contained in a electron microscopy (3DEM) low resolution density map in terms of its available 3D atomic resolution structural components. This fitting process, termed multi-resolution docking, consists in localizing atomic resolution structures into the 3D EM map by means of an exhaustive search of all possible relative rotations and translations.
Bioinformatics/computer Applications in The Biosciences, 2007
DFprot is a web-based server for predicting main-chain deformability from a single protein confor... more DFprot is a web-based server for predicting main-chain deformability from a single protein conformation. The server automatically performs a normal-mode analysis (NMA) of the uploaded structure and calculates its capability to deform at each of its residues. Non-specialists can easily and rapidly obtain a quantitative first approximation of the flexibility of their structures with a simple and efficient interface. Availability: http://sbg.cib.csic.es/Software/DFprot Contact: pablo@cib.csic.es Fig. 1. Snapshot of deformability results using iSee methodology. J.I.Garzó n et al.
Bioinformatics/computer Applications in The Biosciences, 2007
Motivation: Efficient fitting tools are needed to take advantage of a fast growth of atomic model... more Motivation: Efficient fitting tools are needed to take advantage of a fast growth of atomic models of protein domains from crystallography or comparative modeling, and low-resolution density maps of larger molecular assemblies. Here, we report a novel fitting algorithm for the exhaustive and fast overlay of partial high-resolution models into a low-resolution density map. The method incorporates a fast rotational search based on spherical harmonics (SH) combined with a simple translational scanning. Results: This novel combination makes it possible to accurately dock atomic structures into low-resolution electron-density maps in times ranging from seconds to a few minutes. The high-efficiency achieved with simulated and experimental test cases preserves the exhaustiveness needed in these heterogeneous-resolution merging tools. The results demonstrate its efficiency, robustness and high-throughput coverage.
International Journal of High Performance Computing Applications, 2010
Cache techniques are an efficient tool to reduce latency times in transfer operations through Gri... more Cache techniques are an efficient tool to reduce latency times in transfer operations through Grid systems. Although different approximations to introduce cache facilities into Grid computing have already been studied, they require intrusive modifications of Grid software and hardware. Here, we propose an end-to-end cache system that is implemented over scheduling services. This cache system requires neither changes in the Grid software nor introduction of new software in the Grid resources. Parallel Grid adaptation of many high-throughput computing applications that use the same data intensively could enjoy great benefits from our cache system. The maintenance of cacheable data in the resources of already-executed tasks allows faster executions of future tasks assigned to the same resources. To analyze the performance of our endto-end cache system, we tested it with a new protein-protein docking application. The obtained results confirm our cache system's robustness and efficiency gain for this kind of high-throughput application.
... Para las áreas metropolitanas tenemos que la zona que mayor producción bruta tiene es la de B... more ... Para las áreas metropolitanas tenemos que la zona que mayor producción bruta tiene es la de Bogota DC - Soacha, con un 28.9% luego se ubica el área de Medellín – Valle de Aburrá, queparticipa con un 23.1%. Pos-teriormente, la zona de Cali-Yumbo con un 22.8%. ...
Food Policy, 1984
This article reviews the experience of the US Food for Peace Program (PL 480) under Title III, wi... more This article reviews the experience of the US Food for Peace Program (PL 480) under Title III, with the objective of identifying some of the limitations and possibilities of using food aid as a development tool. It will argue that while multi-year agreements are inflexible, the settings in which the agreements are to be implemented are turbulent and uncertain. Combining food aid with development also makes severe demands upon the administrative capacity of both field missions and recipients, resulting in a reluctance on the part of both to initiate agreements.
International Journal of Urban and Regional Research, 1985
Food Policy, 1984
This article reviews the experience of the US Food for Peace Program (PL 480) under Title III, wi... more This article reviews the experience of the US Food for Peace Program (PL 480) under Title III, with the objective of identifying some of the limitations and possibilities of using food aid as a development tool. It will argue that while multi-year agreements are inflexible, the settings in which the agreements are to be implemented are turbulent and uncertain. Combining food aid with development also makes severe demands upon the administrative capacity of both field missions and recipients, resulting in a reluctance on the part of both to initiate agreements.
2014 22nd Euromicro International Conference on Parallel, Distributed, and Network-Based Processing, 2014
The procedure for screening large databases of small chemical compounds to select likely drug can... more The procedure for screening large databases of small chemical compounds to select likely drug candidates by computational means is very time demanding. Here, we present and evaluate a new method for virtual screening (VS) that combines the efficiency of spherical harmonic approximations to accelerate the rotational part of a docking search with multicore and GPU parallelism. To validate these novel parallel algorithms, we used standard benchmark cases. The obtained results are comparable to those generated via state-of-the-art VS docking approximations, but with a considerable gain in efficiency. GPU implementation speedups of more than 30-fold with respect to a single core CPU were achieved, reducing the docking time for a single ligand to only 50 milliseconds. The achieved efficiency and the accuracy on standard blind benchmarks demonstrate the applicability and robustness of this approach.
Bioinformatics/computer Applications in The Biosciences, 2009
Prediction of protein-protein complexes from the coordinates of their unbound components usually ... more Prediction of protein-protein complexes from the coordinates of their unbound components usually starts by generating many potential predictions from a rigid-body 6D search followed by a second stage that aims to refine such predictions. Here, we present and evaluate a new method to effectively address the complexity and sampling requirements of the initial exhaustive search. In this approach we combine the projection of the interaction terms into 3D grid-based potentials with the efficiency of spherical harmonics approximations to accelerate the search. The binding energy upon complex formation is approximated as a correlation function composed of van der Waals, electrostatics and desolvation potential terms. The interaction-energy minima are identified by a novel, fast and exhaustive rotational docking search combined with a simple translational scanning. Results obtained on standard protein-protein benchmarks demonstrate its general applicability and robustness. The accuracy is comparable to that of existing stateof-the-art initial exhaustive rigid-body docking tools, but achieving superior efficiency. Moreover, a parallel version of the method performs the docking search in just a few minutes, opening new application opportunities in the current 'omics' world.
PLoS ONE, 2014
The distance-dependent knowledge-based DrugScore(PPI) potentials, previously developed for in sil... more The distance-dependent knowledge-based DrugScore(PPI) potentials, previously developed for in silico alanine scanning and hot spot prediction on given structures of protein-protein complexes, are evaluated as a scoring and objective function for the structure prediction of protein-protein complexes. When applied for ranking "unbound perturbation" ("unbound docking") decoys generated by Baker and coworkers a 4-fold (1.5-fold) enrichment of acceptable docking solutions in the top ranks compared to a random selection is found. When applied as an objective function in FRODOCK for bound protein-protein docking on 97 complexes of the ZDOCK benchmark 3.0, DrugScore(PPI)/FRODOCK finds up to 10% (15%) more high accuracy solutions in the top 1 (top 10) predictions than the original FRODOCK implementation. When used as an objective function for global unbound protein-protein docking, fair docking success rates are obtained, which improve by ∼ 2-fold to 18% (58%) for an at least acceptable solution in the top 10 (top 100) predictions when performing knowledge-driven unbound docking. This suggests that DrugScore(PPI) balances well several different types of interactions important for protein-protein recognition. The results are discussed in view of the influence of crystal packing and the type of protein-protein complex docked. Finally, a simple criterion is provided with which to estimate a priori if unbound docking with DrugScore(PPI)/FRODOCK will be successful.
Journal of Software, 2007
Rigid body fitting is the common way to interpret the 3D information contained in a electron micr... more Rigid body fitting is the common way to interpret the 3D information contained in a electron microscopy (3DEM) low resolution density map in terms of its available 3D atomic resolution structural components. This fitting process, termed multi-resolution docking, consists in localizing atomic resolution structures into the 3D EM map by means of an exhaustive search of all possible relative rotations and translations.
Bioinformatics/computer Applications in The Biosciences, 2007
DFprot is a web-based server for predicting main-chain deformability from a single protein confor... more DFprot is a web-based server for predicting main-chain deformability from a single protein conformation. The server automatically performs a normal-mode analysis (NMA) of the uploaded structure and calculates its capability to deform at each of its residues. Non-specialists can easily and rapidly obtain a quantitative first approximation of the flexibility of their structures with a simple and efficient interface. Availability: http://sbg.cib.csic.es/Software/DFprot Contact: pablo@cib.csic.es Fig. 1. Snapshot of deformability results using iSee methodology. J.I.Garzó n et al.
Bioinformatics/computer Applications in The Biosciences, 2007
Motivation: Efficient fitting tools are needed to take advantage of a fast growth of atomic model... more Motivation: Efficient fitting tools are needed to take advantage of a fast growth of atomic models of protein domains from crystallography or comparative modeling, and low-resolution density maps of larger molecular assemblies. Here, we report a novel fitting algorithm for the exhaustive and fast overlay of partial high-resolution models into a low-resolution density map. The method incorporates a fast rotational search based on spherical harmonics (SH) combined with a simple translational scanning. Results: This novel combination makes it possible to accurately dock atomic structures into low-resolution electron-density maps in times ranging from seconds to a few minutes. The high-efficiency achieved with simulated and experimental test cases preserves the exhaustiveness needed in these heterogeneous-resolution merging tools. The results demonstrate its efficiency, robustness and high-throughput coverage.
International Journal of High Performance Computing Applications, 2010
Cache techniques are an efficient tool to reduce latency times in transfer operations through Gri... more Cache techniques are an efficient tool to reduce latency times in transfer operations through Grid systems. Although different approximations to introduce cache facilities into Grid computing have already been studied, they require intrusive modifications of Grid software and hardware. Here, we propose an end-to-end cache system that is implemented over scheduling services. This cache system requires neither changes in the Grid software nor introduction of new software in the Grid resources. Parallel Grid adaptation of many high-throughput computing applications that use the same data intensively could enjoy great benefits from our cache system. The maintenance of cacheable data in the resources of already-executed tasks allows faster executions of future tasks assigned to the same resources. To analyze the performance of our endto-end cache system, we tested it with a new protein-protein docking application. The obtained results confirm our cache system's robustness and efficiency gain for this kind of high-throughput application.