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At least 127 records · Page 7
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

A curated benchmark for cofolding models on kinase conformational states

Abstract Protein kinases are critical drug targets, requiring therapeutics that can modulate their active and inactive conformational states. While cofolding models can generate global folds directly from kinase sequences and ligand SMILES strings, these models have not yet been tested on their ability to recover ligand-induced-fit conformational states of the kinase proteins. Here, we introduce KinConfBench, a curated benchmark of 2225 high-quality human kinase chains to evaluate the ability of four state-of-the-art cofolding models—Boltz-2, Chai-1, Protenix, and RoseTTAFold-All-Atom—to recover both canonical and rare conformational states. We show that geometric success metrics of a ligand pose in the active site do not correlate strongly with the correct kinase conformational state, motivating a new set of dynamical benchmarks for assessing cofolding models. While all four cofolding models achieve ~60–80% prediction accuracy for kinase conformational classification, they exhibit severe mode collapse when performing multiple inferences, show negligible structural diversity in sampling induced-fit motions, and display a prevalent “apo-drift” in which most cofolding models predominantly predict the kinase to be in its ligand-free state. Our results highlight that capturing ligand-induced protein conformational diversity, not just geometric fit, is critical for next-generation structure-based drug discovery.

Sun, Kunyang↗
DOE OSTI2025

Metabolic Modification of Sphingobium lignivorans SYK-6 for Lignin Valorization Through the Discovery of an Unusual Transcriptional Repressor of Lignin-Derived Dimer Catabolism

Sphingobium lignivorans SYK-6 catabolizes guaiacylglycerol-..beta..-guaiacyl ether (GGE, a ..beta..-O-4-type dimer) and 1,2-diguaiacylpropane-1,3-diol (DGPD, a ..beta..-1-type dimer) derived from lignin. Recently, SLG_35860 containing TetR- and MarR-type transcriptional regulator motifs was suggested to be involved in the regulation of GGE and DGPD catabolism. Here we investigated the role of SLG_35860 in the transcriptional regulation of GGE and DGPD catabolism genes. SLG_35860 designated ligS repressed 11 genes involved in GGE and DGPD catabolism. LigS binds directly to specific sequences in the promoter region of each gene. The MarR domain was shown to be involved in these bindings; however, GGE, DGPD, and their metabolites did not function as effectors of LigS. We discovered unidentified compound(s) in the black liquor of oxygen-soda anthraquinone pulping of Japanese cedar that SYK-6 cannot metabolize and that acted as effector(s). Therefore, LigS constantly represses the transcription of the GGE and DGPD catabolism genes to low levels. Based on these findings, we examined the productivity of a polymer building block, 2-pyrone-4,6-dicarboxylic acid (PDC), from GGE, DGPD, and a GGE metabolite using an engineered ligS mutant. The rates of PDC production from each compound by this strain were 1.5-6.0 times higher than those of a PDC-producing strain carrying ligS.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

The C2 domain augments Ras GTPase-activating protein catalytic activity

Regulation of Ras GTPases by GTPase-activating proteins (GAPs) is essential for their normal signaling. Nine of the ten GAPs for Ras contain a C2 domain immediately proximal to their canonical GAP domain, and in RasGAP (p120GAP, p120RasGAP;RASA1) mutation of this domain is associated with vascular malformations in humans. Here, we show that the C2 domain of RasGAP is required for full catalytic activity toward Ras. Analyses of the RasGAP C2-GAP crystal structure, AlphaFold models, and sequence conservation reveal direct C2 domain interaction with the Ras allosteric lobe. This is achieved by an evolutionarily conserved surface centered around RasGAP residue R707, point mutation of which impairs the catalytic advantage conferred by the C2 domain in vitro. In mice,R707Cmutation phenocopies the vascular and signaling defects resulting from constitutive disruption of theRASA1gene. In SynGAP, mutation of the equivalent conserved C2 domain surface impairs catalytic activity. Our results indicate that the C2 domain is required to achieve full catalytic activity of GAPs for Ras.

Science & Technology - Other Topics↗
DOE OSTI2026

V-HAMSTeR v1.0.0

V-HAMSTeR is a bioinformatics software tool designed to predict the hosts of viruses directly from genomic sequences. It can be used by researchers to predict animal, prokaryotic, plant, protist or fungal viral hosts including viruses that may be fragmented or discovered in environmental metagenomic datasets. Features & Uses: The software employs a novel dual-stream deep learning architecture that dynamically fuses implicit sequence embeddings from a genomic foundation model with 13 explicit, handcrafted biological features (e.g., coding density and strand switch rates). To ensure maximum reliability, V=HAMSTeR deploys a 5-fold deep ensemble calibrated via Joint Temperature Scaling, providing users with statistically rigorous confidence probabilities. It also features an automated sequence chunking and mean-pooling module to seamlessly process variable-length contigs. Advantages Over Similar Technologies: Existing tools (e.g., IPEV, RNAVirHost) typically rely on either basic k-mers or isolated neural networks. V-HAMSTeR's hybrid architecture captures both broad genomic context and specific biological motifs that standalone foundation models often miss. Furthermore, unlike competitor tools that struggle with incomplete data or exhibit extreme overconfidence, V-HAMSTeR is explicitly benchmarked and mathematically calibrated for fragmented assemblies (1kb–10kb). This makes it uniquely robust, accurate, and trustworthy for the messy reality of real-world environmental viromics.

Grigson, Susie [Lawrence Berkeley National Laborat↗
NASA NTRS1992

Planning Assembly Of Large Truss Structures In Outer Space

Report dicusses developmental algorithm used in systematic planning of sequences of operations in which large truss structures assembled in outer space. Assembly sequence represented by directed graph called "assembly graph", in which each arc represents joining of two parts or subassemblies. Algorithm generates assembly graph, working backward from state of complete assembly to initial state, in which all parts disassembled. Working backward more efficient than working forward because it avoids intermediate dead ends.

De Mello, Luiz S. Homem↗
NASA NTRS1994

Sub-ply level scaling approach investigated for graphite-epoxy composite beam columns

Scale model graphite-epoxy composite specimens were fabricated using the 'sub-ply level' approach and tested as beam-columns under an eccentric axial load to determine the effect of specimen size on flexural response and failure. In the current research project, although the fiber diameters are not scaled, the thickness of the pre-preg material itself has been scaled by adjusting the number of fibers through the thickness of a single ply. Three different grades of graphite-epoxy composite material (AS4/3502) were obtained from Hercules, Inc., in which the number of fibers through the thickness of a single ply was reduced (Grade 190 with 12 to 16 fibers, Grade 95 with 6 to 8 fibers, and Grade 48 with 3 to 4 fibers). Thus, using the sub-ply level approach, a baseline eight ply quasi-isotropic laminate could be fabricated using either the Grade 48 or Grade 95 material and the corresponding full-scale laminate would be constructed from Grade 95 or standard Grade 190 material, respectively. Note that in the sub-ply level approach, the number of ply interfaces is constant for the baseline and full-scale laminates. This is not true for the ply level and sublaminate level scaled specimens. The three grades of graphite-epoxy composite material were used to fabricate scale model beam-column specimens with in-plane dimensions of 0.5*n x 5.75*n, where n=1,2,4 corresponsing to 1/4, 1/2, and full-scale factors. Angle ply, cross ply, and quasi-isotropic laminate stacking sequences were chosen for the investigation and the test matrices for each laminate type are given. Specimens in each laminate family with the same in-plane dimensions but different thicknesses were tested to isolate the influence of the thickness dimension on the flexural response and failure. Also, specific lay-ups were chosen with blocked plies and dispersed plies for each laminate type. Specimens were subjected to an eccentric axial load until failure. The load offset was introduced through a set of hinges which were attached to the platens of a standard load test machine. Three sets of geometrically scaled hinges were used to ensure that scaled loading conditions were applied. This loading condition was chosen because it promotes large flexural deformations and specimens fail at the center of the beam, away from the grip supports. Five channels of data including applied vertical load, end shortening displacement, strain from gages applied back-to-back at the midspan of the beam, and rotation of the hinge from a bubble inclinometer were recorded for each specimen. The beam-column test configuration was used previously to study size effects in ply level scaled composite specimens of the same material system, sizes, and stacking sequences. Thus, a direct comparison between the two scaling approaches is possible. Ply level scaled beam-columns with angle ply, cross ply, and quasi-isotropic lay-ups exhibited no size dependencies in the flexural response, but significant size effects in strength. The reduction in strength with increasing specimen size was not predicted successfully by analysis techniques. It is anticipated that results from this investigation will lead to a better understanding of the strength scale effect in composite structures.

Jackson, Karen E.↗
NASA NTRS1996

Whither microbiology? Phylogenetic trees

The direct cloning and sequencing of genes from uncultured microorganisms in a hot spring suggests that the diversity of life on Earth may be far in excess of that estimated from culturable species.

NASA Discipline Exobiology↗
NASA NTRS2018

The Turbolift: Linear Sled Hybrid Artificial Gravity Concept

Future crewed space exploration missions into deep space will require enhanced countermeasure technologies to ensure astronaut health. One such hazard is extended exposure to reduced gravity levels (i.e., microgravity, lunar gravity, or Martian gravity). Reduced gravity negatively impacts many physiological systems, leading to hydrostatic intolerance, musculoskeletal atrophy, sensorimotor impairment, bone demineralization, cardiovascular deconditioning, and visual alterations. Various countermeasures have been employed for mitigating these effects, such as exercise, pharmaceuticals, diet, and fluid loading. However, these approaches treat individual symptoms, such that each physiological system is addressed with typically one countermeasure. An alternative to this approach is artificial gravity (AG), which promises to be a holistic, comprehensive countermeasure. The traditional approach to creating AG is through centrifugation. However, centrifugation is not a "pure" form of AG and typically includes the drawbacks of Coriolis forces, gravity gradients, and vestibular cross-coupled illusions.As an alternative, we have proposed a Linear Sled Hybrid (LSH) AG system to mitigate astronauts' physiological deconditioning. This system functions by applying pure linear acceleration to produce footward loading. There is a half rotation (180_) to reorient the rider between acceleration and deceleration phases, such that the loading remains footward, as when standing on Earth. The rotation also provides some footward acceleration to the lower body through centripetal acceleration; hence the "hybrid" aspect of the design. At the end of the deceleration, the rider than accelerates back in the opposite direction and the sequence repeats.This proposed system could be integrated with future crewed space vehicles in a variety of manners.

Gruber, Jason↗
NASA NTRS1986

The rRNA evolution and procaryotic phylogeny

Studies of ribosomal RNA primary structure allow reconstruction of phylogenetic trees for prokaryotic organisms. Such studies reveal major dichotomy among the bacteria that separates them into eubacteria and archaebacteria. Both groupings are further segmented into several major divisions. The results obtained from 5S rRNA sequences are essentially the same as those obtained with the 16S rRNA data. In the case of Gram negative bacteria the ribosomal RNA sequencing results can also be directly compared with hybridization studies and cytochrome c sequencing studies. There is again excellent agreement among the several methods. It seems likely then that the overall picture of microbial phylogeny that is emerging from the RNA sequence studies is a good approximation of the true history of these organisms. The RNA data allow examination of the evolutionary process in a semi-quantitative way. The secondary structures of these RNAs are largely established. As a result it is possible to recognize examples of local structural evolution. Evolutionary pathways accounting for these events can be proposed and their probability can be assessed.

Fox, G. E.↗
NASA NTRS1973

Automatic vehicle location system

An automatic vehicle detection system is disclosed, in which each vehicle whose location is to be detected carries active means which interact with passive elements at each location to be identified. The passive elements comprise a plurality of passive loops arranged in a sequence along the travel direction. Each of the loops is tuned to a chosen frequency so that the sequence of the frequencies defines the location code. As the vehicle traverses the sequence of the loops as it passes over each loop, signals only at the frequency of the loop being passed over are coupled from a vehicle transmitter to a vehicle receiver. The frequencies of the received signals in the receiver produce outputs which together represent a code of the traversed location. The code location is defined by a painted pattern which reflects light to a vehicle carried detector whose output is used to derive the code defined by the pattern.

Hansen, G. R., Jr.↗
NASA NTRS2007

Golden Ratio Versus Pi as Random Sequence Sources for Monte Carlo Integration

We discuss here the relative merits of these numbers as possible random sequence sources. The quality of these sequences is not judged directly based on the outcome of all known tests for the randomness of a sequence. Instead, it is determined implicitly by the accuracy of the Monte Carlo integration in a statistical sense. Since our main motive of using a random sequence is to solve real world problems, it is more desirable if we compare the quality of the sequences based on their performances for these problems in terms of quality/accuracy of the output. We also compare these sources against those generated by a popular pseudo-random generator, viz., the Matlab rand and the quasi-random generator ha/ton both in terms of error and time complexity. Our study demonstrates that consecutive blocks of digits of each of these numbers produce a good random sequence source. It is observed that randomly chosen blocks of digits do not have any remarkable advantage over consecutive blocks for the accuracy of the Monte Carlo integration. Also, it reveals that pi is a better source of a random sequence than theta when the accuracy of the integration is concerned.

Sen, S. K.↗
NASA NTRS2002

Session A-14: Variability of Storm Tracks Storm Tracks and Unseasonable Temperatures in Europe in December 2001

In December 2001, a series of cyclonic centers progressed rapidly into Europe from the west and north. The cyclones moved in generally similar directions, along paths separated by few hundreds of kilometers. The advancing cyclones brought the usual sequence of changing wind directions and produced some high speed wind events. We investigate the wind patterns for this month based on analyses derived the Special Sensor Microwave/Imager observations and NCEP analyses. Whereas southwesterlies from the North Atlantic produced moderate temperatures early in the month, strong northerlies and northwesterlies (up to 15 m/s on 20-22 December) produced a drop in daily minimum and maximum temperatures of 18.8 C and 9.9 C, respectively, over a 4 day period (to -18.8 C and -6.8 C, respectively, on December 23 in Torun, Poland). Such low values in December are unprecedented in recent decades, though not for January or February.

Przybylak, R.↗
NASA NTRS2004

Strobe Traffic Lights Warn of Approaching Emergency Vehicles

Strobe-enhanced traffic signals have been developed to aid in the preemption of road intersections for emergency vehicles. The strobe-enhanced traffic signals can be incorporated into both new and pre-existing traffic-control systems in which the traffic-signal heads are of a relatively new type based on arrays of light-emitting diodes (LEDs). The strobe-enhanced traffic signals offer a less expensive, less complex alternative to a recently developed system of LED-based warning signs placed next to traffic signals. Because of its visual complexity, the combination of traffic signals and warning signs is potentially confusing to motorists. The strobe-enhanced traffic signals present less visual clutter. In a given traffic-signal head, the strobe-enhanced traffic signal is embedded in the red LED array of the stop signal. Two strobe LED strips one horizontal and one vertical are made capable of operating separately from the rest of the red LED matrix. When no emergency vehicle is approaching, the red LED array functions as a normal stop signal: all the red LEDs are turned on and off together. When the intersection is to be preempted for an approaching emergency vehicle, only the LEDs in one of the strobe strips are lit, and are turned on in a sequence that indicates the direction of approach. For example (see figure), if an emergency vehicle approaches from the right, the strobe LEDs are lit in a sequence moving from right to left. Important to the success of strobe-enhanced traffic signals is conformance to city ordinances and close relation to pre-existing traffic standards. For instance, one key restriction is that new icons must not include arrows, so that motorists will not confuse new icons with conventional arrows that indicate allowed directions of movement. It is also critical that new displays like strobe-enhanced traffic signals be similar to displays used in traffic-control systems in large cities. For example, Charleston, South Carolina uses horizontal strobes on red traffic lights to alert motorists and thereby help motorists not to miss red lights. The one significant potential disadvantage of strobe-enhanced traffic lights is initial unfamiliarity on the part of motorists.

Bachelder, Aaron↗
NASA NTRS1998

Origin of the catalytic activity of bovine seminal ribonuclease against double-stranded RNA

Bovine seminal ribonuclease (RNase) binds, melts, and (in the case of RNA) catalyzes the hydrolysis of double-stranded nucleic acid 30-fold better under physiological conditions than its pancreatic homologue, the well-known RNase A. Reported here are site-directed mutagenesis experiments that identify the sequence determinants of this enhanced catalytic activity. These experiments have been guided in part by experimental reconstructions of ancestral RNases from extinct organisms that were intermediates in the evolution of the RNase superfamily. It is shown that the enhanced interactions between bovine seminal RNase and double-stranded nucleic acid do not arise from the increased number of basic residues carried by the seminal enzyme. Rather, a combination of a dimeric structure and the introduction of two glycine residues at positions 38 and 111 on the periphery of the active site confers the full catalytic activity of bovine seminal RNase against duplex RNA. A structural model is presented to explain these data, the use of evolutionary reconstructions to guide protein engineering experiments is discussed, and a new variant of RNase A, A(Q28L K31C S32C D38G E111G), which contains all of the elements identified in these experiments as being important for duplex activity, is prepared. This is the most powerful catalyst within this subfamily yet observed, some 46-fold more active against duplex RNA than RNase A.

Non-NASA Center↗
DOE OSTI2022

Selective Whole-Genome Amplification as a Tool to Enrich Specimens with Low Treponema pallidum Genomic DNA Copies for Whole-Genome Sequencing

Downstream next-generation sequencing (NGS) of the syphilis spirochete Treponema pallidum subspecies pallidum (T. pallidum) is hindered by low bacterial loads and the overwhelming presence of background metagenomic DNA in clinical specimens. In this study, we investigated selective whole-genome amplification (SWGA) utilizing multiple displacement amplification (MDA) in conjunction with custom oligonucleotides with an increased specificity for the T. pallidum genome and the capture and removal of 5'-C-phosphate-G-3' (CpG) methylated host DNA using the NEBNext Microbiome DNA enrichment kit followed by MDA with the REPLI-g single cell kit as enrichment methods to improve the yields of T. pallidum DNA in isolates and lesion specimens from syphilis patients. Sequencing was performed using the Illumina MiSeq v2 500 cycle or NovaSeq 6000 SP platform. These two enrichment methods led to 93 to 98% genome coverage at 5 reads/site in 5 clinical specimens from the United States and rabbit-propagated isolates, containing >14 T. pallidum genomic copies/μL of sample for SWGA and >129 genomic copies/μL for CpG methylation capture with MDA. Variant analysis using sequencing data derived from SWGA-enriched specimens showed that all 5 clinical strains had the A2058G mutation associated with azithromycin resistance. SWGA is a robust method that allows direct whole-genome sequencing (WGS) of specimens containing very low numbers of T. pallidum, which has been challenging until now.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Convergence acceleration of Monte Carlo many-body perturbation methods by direct sampling

In the Monte Carlo many-body perturbation (MC-MP) method, the conventional correlation-correction formula, which is a long sum of products of low-dimensional integrals, is first recast into a short sum of high-dimensional integrals over electron-pair and imaginary-time coordinates. These high-dimensional integrals are then evaluated by the Monte Carlo method with random coordinates generated by the Metropolis–Hasting algorithm according to a suitable distribution. The latter algorithm, while advantageous in its ability to sample nearly any distribution, introduces autocorrelation in sampled coordinates, which in turn increases the statistical uncertainty of the integrals and thus the computational cost. It also involves wasteful rejected moves and an initial “burn-in” step as well as displays hysteresis. Here, an algorithm is proposed that directly produces a random sequence of electron-pair coordinates for the same distribution used in the MC-MP method, which is free from autocorrelation, rejected moves, a burn-in step, or hysteresis. Furthermore, this direct-sampling algorithm is shown to accelerate second- (MC-MP2) and third-order Monte Carlo many-body perturbation (MC-MP3) calculations by up to 222% and 38%, respectively.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1990

Generation of animation sequences of three dimensional models

The invention is directed toward a method and apparatus for generating an animated sequence through the movement of three-dimensional graphical models. A plurality of pre-defined graphical models are stored and manipulated in response to interactive commands or by means of a pre-defined command file. The models may be combined as part of a hierarchical structure to represent physical systems without need to create a separate model which represents the combined system. System motion is simulated through the introduction of translation, rotation and scaling parameters upon a model within the system. The motion is then transmitted down through the system hierarchy of models in accordance with hierarchical definitions and joint movement limitations. The present invention also calls for a method of editing hierarchical structure in response to interactive commands or a command file such that a model may be included, deleted, copied or moved within multiple system model hierarchies. The present invention also calls for the definition of multiple viewpoints or cameras which may exist as part of a system hierarchy or as an independent camera. The simulated movement of the models and systems is graphically displayed on a monitor and a frame is recorded by means of a video controller. Multiple movement and hierarchy manipulations are then recorded as a sequence of frames which may be played back as an animation sequence on a video cassette recorder.

Poi, Sharon↗