Electrostatic-field and surface-shape similarity for virtual screening and pose prediction.

We introduce a new method for rapid computation of 3D molecular similarity that combines electrostatic field comparison with comparison of molecular surface-shape and directional hydrogen-bonding preferences (called "eSim"). Rather than employing heuristic "colors" or user-defined molecular feature types to represent conformation-dependent molecular electrostatics, eSim calculates the similarity of the electrostatic fields of two molecules (in addition to shape and hydrogen-bonding). We present detailed virtual screening performance data on the standard 102 target DUD-E set. In its moderately fast screening mode, eSim running on a single computing core is capable of processing over 60 molecules per second. In this mode, eSim performed significantly better than all alternate methods for which full DUD-E data were available (mean ROC area of 0.74, p [Formula: see text], by paired t-test, compared with the best performing alternate method). In addition, for 92 targets of the DUD-E set where multiple ligand-bound crystal structures were available, screening performance was assessed using alternate ligands or sets thereof (in their bound poses) as similarity targets. Using the joint alignment of five ligands for each protein target, mean ROC area exceeded 0.82 for the 92 targets. Design-focused application of ligand similarity methods depends on accurate predictions of geometric molecular relationships. We comprehensively assessed pose prediction accuracy by curating nearly 400,000 bound ligand pose pairs across the DUD-E targets. Overall, beginning from agnostic initial poses, we observed an 80% success rate for RMSD [Formula: see text] Å  among the top 20 predicted eSim poses. These examples were split roughly 50/50 into cases with high direct atomic overlap (where a shared scaffold exists between a pair) and low direct atomic overlap (where where a ligand pair has dissimilar scaffolds but largely occupies the same space). Within the high direct atomic overlap subset, the pose prediction success rate was 93%. For the more challenging subset (where dissimilar scaffolds are to be aligned), the success rate was 70%. The eSim approach enables both large-scale screening and rational design of ligands and is rooted in physically meaningful, non-heuristic, molecular comparisons

Fall Observations of Westward Migrating White Whales (Delphinapterus leucas) Along the Central Alaskan Beaufort Sea Coast

... it appears that at least a portion of the westward fall migration by white whales out of the southeastern Beaufort Sea occurs during mid-to late September near the coast, well south of the southern edge of the pack-ice, but seaward of the barrier islands. ..

Staging and Wintering Areas of Snow Geese Nesting on Howe Island, Alaska

From July 1980 to July 1990, leg bands were put on 4556 adults, subadults, and goslings from the lesser snow goose (Chen caerulescens caerulescens) colony (~1000 nesting birds) on Howe Island, near Prudhoe Bay, Alaska. In addition, 1431 neck bands were put on 1714 of the leg-banded adults and subadults. During the period from September 1980 through May 1991, 3244 discrete, within-year resightings and recoveries were received of neck-banded and leg-banded birds during fall, winter, early spring, and late spring. During mid to late August each year, the Howe Island geese migrated eastward from the Prudhoe Bay area to staging/feeding areas in the Arctic National Wildlife Refuge, Alaska and in adjacent areas of the Yukon Territory. In mid to late September they moved southward down the Mackenzie Valley. Cluster analyses for the ten-year period 1980-90 revealed six separate distribution loci for the geese during the fall, with the largest proportion (84.7%) in one location in southeastern Alberta and southwestern Saskatchewan. Analyses revealed 11 separate distribution loci for the geese during winter from 1980 to 1991; the largest proportion (79.2%) was in northern California and southern Oregon. There were seven different distribution loci for the geese during early spring from 1981 to 1991; the largest proportion was in northern California and southeastern Oregon (81.4%). There were five distinct aggregations of the Howe Island geese during late spring from 1981 to 1991, with the largest proportion (79.1%) in staging/feeding areas in Montana, Alberta, and Saskatchewan. Most geese in both flyways were faithful to specific overwintering locations from one year to the next. Of 262 birds for which year-to-year data were available, 98% in the Pacific Flyway returned to the same region in subsequent winters, and 90% in the Central Flyway returned to the same region. Nevertheless, some geese from both flyways moved to the other flyway during subsequent winters, and a few moved from the Pacific to the Central Flyway during the same winter. In general, the migration routes and overwintering areas of the Howe Island snow geese formed a pattern similar to that documented several decades ago for the much larger Western Arctic population, which nests mainly on Banks Island, Northwest Territories, Canada. The Howe Island geese are likely a satellite colony of the Western Arctic population.De juillet 1980 à juillet 1990, des bagues ont été posées aux pattes de 4556 petites oies des neiges (Chen caerulescens caerulescens) adultes, jeunes adultes et oisons faisant partie de la colonie (~1000 oiseaux nicheurs) de l'île Howe, près de Prudhoe Bay en Alaska. En outre, 1431 colliers ont été posés à 1714 des adultes et jeunes adultes déjà bagués. En automne, en hiver, au début et à la fin du printemps, durant la période allant de septembre 1980 à mai 1991, on a enregistré 3244 occurrences distinctes où des oiseaux bagués aux pattes et au cou ont été réaperçus dans l'année ou récupérés. Chaque année, durant la deuxième quinzaine d'août, les oies de l'île Howe migrent vers l'est depuis la région de Prudhoe Bay en direction des aires de repos / de nutrition du Arctic National Wildlife Refuge situé en Alaska et dans des régions avoisinantes du Territoire du Yukon. Durant la deuxième quinzaine de septembre, elles se déplaçaient vers le sud en suivant la vallée du Mackenzie. Des analyses typologiques portant sur la décennie allant de 1980 à 1990 ont révélé six lieux distincts où se répartissaient les oies au cours de l'automne, la proportion la plus importante (84,7 p. cent) se trouvant dans un site du sud-est de l'Alberta et du sud-ouest de la Saskatchewan. Les analyses montrent qu'il existe 11 lieux distincts où se répartissaient les oies durant l'hiver entre 1980 et 1991; la proportion la plus importante (79,2 p. cent) se trouvait dans le nord de la Californie et le sud de l'Oregon. Au début du printemps, de 1981 à 1991, il y avait sept sites différents où se répartissaient les oies; la plus grande proportion se trouvait dans le nord de la Californie et le sud-est de l'Oregon (81,4 p. cent). À la fin du printemps, de 1981 à 1991, les oies de l'île Howe composaient cinq concentrations distinctes, la plus grande proportion (79,1 p. cent) se trouvant dans les aires de repos / de nutrition du Montana, de l'Alberta et de la Saskatchewan. La plupart des oies empruntant les deux voies migratoires étaient fidèles à des sites d'hivernage spécifiques d'une année à l'autre. Sur les 262 oiseaux pour lesquels des données d'une année à l'autre étaient disponibles, 98 p. cent de ceux empruntant la voie du Pacifique revenaient dans la même région les hivers suivants, et 90 p. cent de ceux empruntant la voie du Centre revenaient dans la même région. Cependant, certaines oies empruntant l'une ou l'autre des routes changeaient de voie au cours des hivers suivants, et quelques-unes passaient de la voie du Pacifique à la voie du Centre durant le même hiver. En général, les voies de migration et les zones d'hivernage de l'oie des neiges de l'île Howe offrent un schéma similaire à celui rapporté il y a plusieurs dizaines d'années pour la population beaucoup plus nombreuse de l'Arctique occidental, qui niche surtout dans l'île Banks située dans les Territoires du Nord-Ouest (Canada). L'oie de l'île Howe est probablement une colonie satellite de la population de l'Arctique occidental

Distribution and Movements of Brood-rearing Lesser Snow Geese in Relation to Petroleum Development in Arctic Alaska

Environmental scientists were concerned that construction of the Endicott Project in the outer Sagavanirktok River delta, east of Prudhoe Bay, Alaska, would obstruct brood-rearing movements of Alaska's largest established nesting population of lesser snow geese (Chen caerulescens caerulescens). During 1980-84, prior to the Endicott Project, the distribution of snow goose flocks during the brood-rearing period was generally less than 5 km from the coast and 15 km from the nesting colony. Prior to development, the average distance between brood-rearing areas used during consecutive years by individual banded birds was 4.7±2.9 km (mean ±s.d.). After development commenced during winter 1984-85, the distribution of brood-rearing flocks expanded inland as far as 9 km and eastward as far as 32 km from the nesting colony. The average distance between brood-rearing areas used during consecutive years by individual banded birds was 8.0±7.5 km. The proportion of brood-rearing snow geese captured on the east side of the Endicott Road and Causeway (east of the nesting colony) during the post-construction years (1985-93) was not significantly different from the proportion using the same area before construction (1980-84). The hypothesis that the Endicott Road and Causeway obstructed eastward movements of brood-rearing snow geese can be rejected.Les spécialistes de l'environnement s'inquétaient que la construction du pont-jetée Endicott dans le delta externe du Sagavanirktok situé à l'est de Prudhoe Bay en Alaska puisse gêner les déplacements reliés à l'élevage des oisons de la plus importante population nicheuse de la petite oie des neiges (Chen caerulescens caerulescens) en Alaska. Durant la période allant de 1980 à 1984, soit avant le projet Endicott, la distribution des volées d'oies des neiges durant la période d'élevage de la couvée s'étendait en général à moins de 5 km de la côte et 15 km de la colonie nicheuse. Avant la mise en valeur, la distance moyenne entre les zones d'élevage des oisons utilisées durant des années consécutives par des individus bagués était de 4,7 ± 2,9 km (moyenne ± écart-type). Durant l'hiver de 1984-85, après le début de la mise en valeur, la distribution des volées en train d'élever des oisons s'est élargie à l'intérieur des terres jusqu'à 9 km et, vers l'est, jusqu'à 32 km de la colonie nicheuse. La distance moyenne entre les zones d'élevage des oisons utilisées durant des années consécutives par des individus bagués était de 8,0 ± 7,5 km. La proportion d'oies des neiges en train d'élever des oisons capturées à l'est de la route et du pont-jetée Endicott (situés à l'est de la colonie nicheuse) durant les années suivant la construction (1985-93) n'était pas sensiblement différente de la proportion qui utilisait la même région avant la construction (1980-84). On rejette l'hypothèse que la route et le pont-jetée Endicott ont gêné les déplacements vers l'est de l'oie des neiges en période d'élevage

Determination of lunar ilmenite abundances from remotely sensed data

The mineral ilmenite (FeTiO3) was found in abundance in lunar mare soils returned during the Apollo project. Lunar ilmenite often contains greater than 50 weight-percent titanium dioxide (TiO2), and is a primary potential resource for oxygen and other raw materials to supply future lunar bases. Chemical and spectroscopic analysis of the returned lunar soils produced an empirical function that relates the spectral reflectance ratio at 400 and 560 nm to the weight percent abundance of TiO2. This allowed mapping of the lunar TiO2 distribution using telescopic vidicon multispectral imaging from the ground; however, the time variant photometric response of the vidicon detectors produced abundance uncertainties of at least 2 to 5 percent. Since that time, solid-state charge-coupled device (CCD) detector technology capable of much improved photometric response has become available. An investigation of the lunar TiO2 distribution was carried out utilizing groundbased telescopic CCD multispectral imagery and spectroscopy. The work was approached in phases to develop optimum technique based upon initial results. The goal is to achieve the best possible TiO2 abundance maps from the ground as a precursor to lunar orbiter and robotic sample return missions, and to produce a better idea of the peak abundances of TiO2 for benefaction studies. These phases and the results are summarized