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Jose L Medinafranco - One of the best experts on this subject based on the ideXlab platform.
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activity Landscape plotter a web based application for the analysis of structure activity relationships
Journal of Chemical Information and Modeling, 2017Co-Authors: Mariana Gonzalezmedina, Oscar Mendezlucio, Jose L MedinafrancoAbstract:Activity Landscape Modeling is a powerful method for the quantitative analysis of structure–activity relationships. This cheminformatics area is in continuous growth, and several quantitative and visual approaches are constantly being developed. However, these approaches often fall into disuse due to their limited access. Herein, we present Activity Landscape Plotter as the first freely available web-based tool to automatically analyze structure–activity relationships of compound data sets. Based on the concept of activity Landscape Modeling, the online service performs pairwise structure and activity relationships from an input data set supplied by the user. For visual analysis, Activity Landscape Plotter generates Structure–Activity Similarity and Dual-Activity Difference maps. The user can interactively navigate through the maps and export all the pairwise structure–activity information as comma delimited files. Activity Landscape Plotter is freely accessible at https://unam-shiny-difacquim.shinyapps.i...
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activity and property Landscape Modeling is at the interface of chemoinformatics and medicinal chemistry
Future Medicinal Chemistry, 2015Co-Authors: Jose L Medinafranco, Gabriel Navarretevazquez, Oscar MendezlucioAbstract:Property Landscape Modeling (PLM) methods are at the interface of experimental sciences and computational chemistry. PLM are becoming a common strategy to describe systematically structure–property relationships of datasets. Thus far, PLM have been used mainly in medicinal chemistry and drug discovery. Herein, we survey advances on key topics on PLM with emphasis on questions often raised regarding the outcomes of the property Landscape studies. We also emphasize on concepts of PLM that are being extended to other experimental areas beyond drug discovery. Topics discussed in this paper include applications of PLM to further characterize protein–ligand interactions, the utility of PLM as a quantitative and descriptive approach, and the statistical validation of property cliffs.
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analyzing multitarget activity Landscapes using protein ligand interaction fingerprints interaction cliffs
Journal of Chemical Information and Modeling, 2015Co-Authors: Oscar Mendezlucio, Albert J Kooistra, Chris De Graaf, Andreas Bender, Jose L MedinafrancoAbstract:Activity Landscape Modeling is mostly a descriptive technique that allows rationalizing continuous and discontinuous SARs. Nevertheless, the interpretation of some Landscape features, especially of activity cliffs, is not straightforward. As the nature of activity cliffs depends on the ligand and the target, information regarding both should be included in the analysis. A specific way to include this information is using protein-ligand interaction fingerprints (IFPs). In this paper we report the activity Landscape Modeling of 507 ligand-kinase complexes (from the KLIFS database) including IFP, which facilitates the analysis and interpretation of activity cliffs. Here we introduce the structure-activity-interaction similarity (SAIS) maps that incorporate information on ligand-target contact similarity. We also introduce the concept of interaction cliffs defined as ligand-target complexes with high structural and interaction similarity but have a large potency difference of the ligands. Moreover, the information retrieved regarding the specific interaction allowed the identification of activity cliff hot spots, which help to rationalize activity cliffs from the target point of view. In general, the information provided by IFPs provides a structure-based understanding of some activity Landscape features. This paper shows examples of analyses that can be carried out when IFPs are added to the activity Landscape model.
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chemoinformatic characterization of activity and selectivity switches of antiprotozoal compounds
Future Medicinal Chemistry, 2014Co-Authors: Rodrigo Aguayoortiz, Jaime Perezvillanueva, Alicia Hernandezcampos, Rafael Castillo, Nathalie Meurice, Jose L MedinafrancoAbstract:Background: Benzimidazole derivatives are promising compounds for the treatment of parasitic infections. The structure–activity relationships of 91 benzimidazoles with activity against Trichomonas vaginalis and Giardia intestinalis were analyzed using a novel activity Landscape Modeling approach. Results: We identified two prominent cases of ‘activity switches‘ and ‘selectivity switches‘ where two R group substitutions in the benzimidazole scaffold completely invert the activity and selectivity pattern for T. vaginalis and G. intestinalis. Conclusion: A chemoinformatic methodology was used to rapidly identify discrete structural changes around the central scaffold that are associated with large changes in biological activity for each parasite. The structure–activity relationships for the benzimidazole derivatives is smooth for both protozoan with few but markedly important activity cliffs.
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scanning structure activity relationships with structure activity similarity and related maps from consensus activity cliffs to selectivity switches
Journal of Chemical Information and Modeling, 2012Co-Authors: Jose L MedinafrancoAbstract:Systematic description of structure–activity relationships (SARs) of data sets and structure–property relationships (SPRs) is of paramount importance in medicinal chemistry and other research fields. To this end, structure–activity similarity (SAS) maps are one of the first tools proposed to describe SARs using the concept of activity Landscape Modeling. One of the major goals of the SAS maps is to identify activity cliffs defined as chemical compounds with high similar structure but unexpectedly very different biological activity. Since the first publication of the SAS maps more than ten years ago, these tools have evolved and adapted over the years to analyze various types of compound collections, including structural diverse and combinatorial sets with activity for one or multiple biological end points. The development of SAS maps has led to general concepts that are applicable to other activity Landscape methods such as “consensus activity cliffs” (activity cliffs common to a series of representations...
David R Montgomery - One of the best experts on this subject based on the ideXlab platform.
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surface roughness dating of long runout landslides near oso washington usa reveals persistent postglacial hillslope instability
Geology, 2016Co-Authors: Sean Richard Lahusen, Adam M Booth, Alison R Duvall, David R MontgomeryAbstract:Establishing regional landslide chronologies is necessary to advance from hazard recognition to risk assessment, and to understand the evolution of landslide-prone terrain. Despite recent advances in landslide mapping due to the availability of high-resolution lidar imagery, estimating the timing of slope failures remains a challenge. Here we present a new integrated approach to dating landslides on a regional scale by augmenting quantitative surface roughness analysis with radiocarbon dating and numerical Landscape Modeling. We calibrate a roughness-age curve, which we use to date 25 deep-seated landslides in glacial sediment surrounding the catastrophic A.D. 2014 Oso landslide along the North Fork Stillaguamish River in Washington State (USA). Lidar bare-earth images show a high density of long-runout landslides in this region. Using our roughness-age curve, we estimate an average Holocene landslide frequency of 1 every 140–500 yr, and show that the 2014 Oso landslide was the latest event in an active history of slope failures throughout the Holocene. With each landslide, substantial sediment is delivered to the North Fork Stillaguamish River, driving shifts in the active channel that ultimately affect the pattern of landslides across the valley. The high frequency of landslides in this area, where river incision and isostatic uplift rates have dropped dramatically since peaking soon after ice retreated from the region, shows that Landscapes inundated by glacial sediment do not require dramatic changes in base level to remain highly unstable for tens of thousands of years.
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surface roughness dating of long runout landslides near oso washington usa reveals persistent postglacial hillslope instability
Geology, 2016Co-Authors: Sean Richard Lahusen, Adam M Booth, Alison R Duvall, David R MontgomeryAbstract:Establishing regional landslide chronologies is necessary to advance from hazard recognition to risk assessment, and to understand the evolution of landslide-prone terrain. Despite recent advances in landslide mapping due to the availability of high-resolution lidar imagery, estimating the timing of slope failures remains a challenge. Here we present a new integrated approach to dating landslides on a regional scale by augmenting quantitative surface roughness analysis with radiocarbon dating and numerical Landscape Modeling. We calibrate a roughness-age curve, which we use to date 25 deep-seated landslides in glacial sediment surrounding the catastrophic A.D. 2014 Oso landslide along the North Fork Stillaguamish River in Washington State (USA). Lidar bare-earth images show a high density of long-runout landslides in this region. Using our roughness-age curve, we estimate an average Holocene landslide frequency of 1 every 140–500 yr, and show that the 2014 Oso landslide was the latest event in an active history of slope failures throughout the Holocene. With each landslide, substantial sediment is delivered to the North Fork Stillaguamish River, driving shifts in the active channel that ultimately affect the pattern of landslides across the valley. The high frequency of landslides in this area, where river incision and isostatic uplift rates have dropped dramatically since peaking soon after ice retreated from the region, shows that Landscapes inundated by glacial sediment do not require dramatic changes in base level to remain highly unstable for tens of thousands of years.
David J Mladenoff - One of the best experts on this subject based on the ideXlab platform.
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design development and application of landis ii a spatial Landscape simulation model with flexible temporal and spatial resolution
Ecological Modelling, 2007Co-Authors: Robert M Scheller, James B Domingo, Brian R Sturtevant, Jeremy S Williams, Arnold Rudy, Eric J Gustafson, David J MladenoffAbstract:We introduce LANDIS-II, a Landscape model designed to simulate forest succession and disturbances. LANDIS-II builds upon and preserves the functionality of previous LANDIS forest Landscape simulation models. LANDIS-II is distinguished by the inclusion of variable time steps for different ecological processes; our use of a rigorous development and testing process used by software engineers; and an emphasis on collaborative features including a flexible, open architecture. We detail the variable time step logic and provide an overview of the system architecture. Finally, we demonstrate model behavior and sensitivity to variable time steps through application to a large boreal forest Landscape. We simulated pre-industrial forest fire regimes in order to establish base-line conditions for future management. Differing model time steps substantially altered our estimates of preindustrial forest conditions. Where disturbance frequency is relatively high or successional processes long, the variable time steps may be a critical element for successful forest Landscape Modeling.
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exploring component based approaches in forest Landscape Modeling
Environmental Modelling and Software, 2002Co-Authors: David R Larsen, David J MladenoffAbstract:Forest management issues are increasingly required to be addressed in a spatial context, which has led to the development of spatially explicit forest Landscape models. The numerous processes, complex spatial interactions, and diverse applications in spatial Modeling make the development of forest Landscape models difficult for any single research group. New developments in componentbased Modeling approaches provide a viable solution. Component-based Modeling breaks a monolithic model into small, interchangeable, and binary components. They have these advantages compared to the traditional Modeling work: 1) developing a component is a much smaller task than developing a whole model, 2) a component can be developed using most programming languages, since the interface format is binary, and 3) new components can replace the existing ones under the same model framework; this reduces the duplication and allows the Modeling community to focus resources on the common products, and to compare results. In this paper, we explore the design of a spatially explicit forest Landscape model in a component-based Modeling framework, based on our work on object-oriented forest Landscape Modeling. We examine the representation of the major components and the interactions between them. Our goal is to facilitate the use of the component-based Modeling approach at the early stage of spatially explicit Landscape Modeling. 2002 Elsevier Science Ltd. All rights reserved.
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spatial Modeling of forest Landscape change approaches and applications
Agricultural and Forest Meteorology, 1999Co-Authors: David J Mladenoff, W L BakerAbstract:Preface 1. Development of forest and Landscape Modeling approaches David J. Mladenoff and William L. Baker 2. Modeling the competitive dynamics and distribution of tree species along moisture gradients John P. Caspersen, John A. Silander, Jr., Charles D. Canham and Stephen W. Pascala 3. Spatial and temporal impacts of adjacent areas on the dynamics of species diversity in a primary forest Jianguo Liu, Kalan Ickes, Peter S. Ashton, James V. La Frankie and N. Manokaran 4. Scaling fine-scale processes to large-scale patterns using models derived from models: meta-models Dean L. Urban, Miguel F. Acevedo and Steven L. Garman 5. Simulating Landscape vegetation dynamics of Bryce Canyon National Park with the vital attributes/fuzzy systems model VAFS/LANDSIM David W. Roberts and David W. Betz 6. Design and behavior of LANDIS, an object-oriented model of forest Landscape disturbance and succession David J. Mladenoff and Hong S. He 7. Predicting forest fire effects at Landscape scales Robert H. Gardner, William H. Romme and Monica G. Turner 8. Mechanistic Modeling of Landscape fire patterns Mark A. Finney 9. Achieving sustainable forest structures on fire-prone Landscapes while pursuing multiple goals John Sessions, K. Norman Johnson, Jerry F. Franklin and John T. Gabriel 10. Modeling the driving factors and ecological consequences of deforestation in the Brazilian Amazon Virginia H. Dale and Scott M. Pearson 11. Spatial simulation of the effects of human and natural disturbance regimes on Landscape structure William L. Baker 12. HARVEST: linking timber harvesting strategies to Landscape patterns Eric J. Gustafson and Thomas R. Crow 13. Progress and future directions in spatial Modeling of forest Landscapes William L. Baker and David J. Mladenoff.
Sean Richard Lahusen - One of the best experts on this subject based on the ideXlab platform.
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surface roughness dating of long runout landslides near oso washington usa reveals persistent postglacial hillslope instability
Geology, 2016Co-Authors: Sean Richard Lahusen, Adam M Booth, Alison R Duvall, David R MontgomeryAbstract:Establishing regional landslide chronologies is necessary to advance from hazard recognition to risk assessment, and to understand the evolution of landslide-prone terrain. Despite recent advances in landslide mapping due to the availability of high-resolution lidar imagery, estimating the timing of slope failures remains a challenge. Here we present a new integrated approach to dating landslides on a regional scale by augmenting quantitative surface roughness analysis with radiocarbon dating and numerical Landscape Modeling. We calibrate a roughness-age curve, which we use to date 25 deep-seated landslides in glacial sediment surrounding the catastrophic A.D. 2014 Oso landslide along the North Fork Stillaguamish River in Washington State (USA). Lidar bare-earth images show a high density of long-runout landslides in this region. Using our roughness-age curve, we estimate an average Holocene landslide frequency of 1 every 140–500 yr, and show that the 2014 Oso landslide was the latest event in an active history of slope failures throughout the Holocene. With each landslide, substantial sediment is delivered to the North Fork Stillaguamish River, driving shifts in the active channel that ultimately affect the pattern of landslides across the valley. The high frequency of landslides in this area, where river incision and isostatic uplift rates have dropped dramatically since peaking soon after ice retreated from the region, shows that Landscapes inundated by glacial sediment do not require dramatic changes in base level to remain highly unstable for tens of thousands of years.
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surface roughness dating of long runout landslides near oso washington usa reveals persistent postglacial hillslope instability
Geology, 2016Co-Authors: Sean Richard Lahusen, Adam M Booth, Alison R Duvall, David R MontgomeryAbstract:Establishing regional landslide chronologies is necessary to advance from hazard recognition to risk assessment, and to understand the evolution of landslide-prone terrain. Despite recent advances in landslide mapping due to the availability of high-resolution lidar imagery, estimating the timing of slope failures remains a challenge. Here we present a new integrated approach to dating landslides on a regional scale by augmenting quantitative surface roughness analysis with radiocarbon dating and numerical Landscape Modeling. We calibrate a roughness-age curve, which we use to date 25 deep-seated landslides in glacial sediment surrounding the catastrophic A.D. 2014 Oso landslide along the North Fork Stillaguamish River in Washington State (USA). Lidar bare-earth images show a high density of long-runout landslides in this region. Using our roughness-age curve, we estimate an average Holocene landslide frequency of 1 every 140–500 yr, and show that the 2014 Oso landslide was the latest event in an active history of slope failures throughout the Holocene. With each landslide, substantial sediment is delivered to the North Fork Stillaguamish River, driving shifts in the active channel that ultimately affect the pattern of landslides across the valley. The high frequency of landslides in this area, where river incision and isostatic uplift rates have dropped dramatically since peaking soon after ice retreated from the region, shows that Landscapes inundated by glacial sediment do not require dramatic changes in base level to remain highly unstable for tens of thousands of years.
Alison R Duvall - One of the best experts on this subject based on the ideXlab platform.
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off fault deformation rate along the southern san andreas fault at mecca hills southern california inferred from Landscape Modeling of curved drainages
Geology, 2018Co-Authors: Harrison J Gray, Alison R Duvall, Charles M Shobe, Daniel E J Hobley, Gregory E Tucker, Sarah A Harbert, Lewis A OwenAbstract:Quantifying off-fault deformation (OFD) rates on geomorphic timescales (10^2-10^5 yr) along strike-slip faults is critical for resolving discrepancies between geologic and geodetic slip-rate estimates, improving knowledge of seismic hazard, and understanding the influence of tectonic motion on Landscapes. Quantifying OFD over these timescales is challenging without displacement markers such as offset terraces or geologic contacts. We present a Landscape evolution model coupled with distributed lateral tectonic shear to show how drainage basins sheared by lateral tectonic motion can reveal OFD rates. The model shows that OFD rate can control the orientation of drainage basin topography: the faster the OFD rate, the greater the deflection of drainage basins towards a fault-parallel orientation. We apply the model to the southern San Andreas Fault near the Mecca Hills, where drainages basins change in orientation with proximity to the fault. Comparison of observed and modeled topography suggests that the OFD rate in the Mecca Hills follows an exponential-like spatial pattern with a maximum rate nearest the fault of 3.5 ± 1.5 mm/yr, which decays to approximately zero at ~600 m distance from the fault. This rate is applicable since the initiation of differential rock uplift in the Mecca Hills at approximately 760 ka. Our results suggest that OFD in this 800 m study area may be as high as 10% of total plate motion. This example demonstrates that curved drainage basins may be used to estimate OFD rates along strike slip faults.
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surface roughness dating of long runout landslides near oso washington usa reveals persistent postglacial hillslope instability
Geology, 2016Co-Authors: Sean Richard Lahusen, Adam M Booth, Alison R Duvall, David R MontgomeryAbstract:Establishing regional landslide chronologies is necessary to advance from hazard recognition to risk assessment, and to understand the evolution of landslide-prone terrain. Despite recent advances in landslide mapping due to the availability of high-resolution lidar imagery, estimating the timing of slope failures remains a challenge. Here we present a new integrated approach to dating landslides on a regional scale by augmenting quantitative surface roughness analysis with radiocarbon dating and numerical Landscape Modeling. We calibrate a roughness-age curve, which we use to date 25 deep-seated landslides in glacial sediment surrounding the catastrophic A.D. 2014 Oso landslide along the North Fork Stillaguamish River in Washington State (USA). Lidar bare-earth images show a high density of long-runout landslides in this region. Using our roughness-age curve, we estimate an average Holocene landslide frequency of 1 every 140–500 yr, and show that the 2014 Oso landslide was the latest event in an active history of slope failures throughout the Holocene. With each landslide, substantial sediment is delivered to the North Fork Stillaguamish River, driving shifts in the active channel that ultimately affect the pattern of landslides across the valley. The high frequency of landslides in this area, where river incision and isostatic uplift rates have dropped dramatically since peaking soon after ice retreated from the region, shows that Landscapes inundated by glacial sediment do not require dramatic changes in base level to remain highly unstable for tens of thousands of years.
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surface roughness dating of long runout landslides near oso washington usa reveals persistent postglacial hillslope instability
Geology, 2016Co-Authors: Sean Richard Lahusen, Adam M Booth, Alison R Duvall, David R MontgomeryAbstract:Establishing regional landslide chronologies is necessary to advance from hazard recognition to risk assessment, and to understand the evolution of landslide-prone terrain. Despite recent advances in landslide mapping due to the availability of high-resolution lidar imagery, estimating the timing of slope failures remains a challenge. Here we present a new integrated approach to dating landslides on a regional scale by augmenting quantitative surface roughness analysis with radiocarbon dating and numerical Landscape Modeling. We calibrate a roughness-age curve, which we use to date 25 deep-seated landslides in glacial sediment surrounding the catastrophic A.D. 2014 Oso landslide along the North Fork Stillaguamish River in Washington State (USA). Lidar bare-earth images show a high density of long-runout landslides in this region. Using our roughness-age curve, we estimate an average Holocene landslide frequency of 1 every 140–500 yr, and show that the 2014 Oso landslide was the latest event in an active history of slope failures throughout the Holocene. With each landslide, substantial sediment is delivered to the North Fork Stillaguamish River, driving shifts in the active channel that ultimately affect the pattern of landslides across the valley. The high frequency of landslides in this area, where river incision and isostatic uplift rates have dropped dramatically since peaking soon after ice retreated from the region, shows that Landscapes inundated by glacial sediment do not require dramatic changes in base level to remain highly unstable for tens of thousands of years.
