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DOE OSTI2024

An artificial intelligence accelerated virtual screening platform for drug discovery

Abstract Structure-based virtual screening is a key tool in early drug discovery, with growing interest in the screening of multi-billion chemical compound libraries. However, the success of virtual screening crucially depends on the accuracy of the binding pose and binding affinity predicted by computational docking. Here we develop a highly accurate structure-based virtual screen method, RosettaVS, for predicting docking poses and binding affinities. Our approach outperforms other state-of-the-art methods on a wide range of benchmarks, partially due to our ability to model receptor flexibility. We incorporate this into a new open-source artificial intelligence accelerated virtual screening platform for drug discovery. Using this platform, we screen multi-billion compound libraries against two unrelated targets, a ubiquitin ligase target KLHDC2 and the human voltage-gated sodium channel Na V 1.7. For both targets, we discover hit compounds, including seven hits (14% hit rate) to KLHDC2 and four hits (44% hit rate) to Na V 1.7, all with single digit micromolar binding affinities. Screening in both cases is completed in less than seven days. Finally, a high resolution X-ray crystallographic structure validates the predicted docking pose for the KLHDC2 ligand complex, demonstrating the effectiveness of our method in lead discovery.

Science & Technology - Other Topics↗

DOE OSTI2025

SANE: strategic autonomous non-smooth exploration for multiple optima discovery in multi-modal and non-differentiable black-box functions

Both computational and experimental material discovery bring forth the challenge of exploring multidimensional and multimodal parameter spaces, such as phase diagrams of Hamiltonians with multiple interactions, composition spaces of combinatorial libraries, material structure image spaces, and molecular embedding spaces. Often these systems are black-boxes and time-consuming to evaluate, which resulted in strong interest towards active learning methods such as Bayesian optimization (BO). However, these systems are often noisy which make the black box function severely multi-modal and non-differentiable, where a vanilla BO can get overly focused near a single or faux optimum, deviating from the broader goal of scientific discovery. To address these limitations, here we developed Strategic Autonomous Non-Smooth Exploration (SANE) to facilitate an intelligent Bayesian optimized navigation with a proposed cost-driven probabilistic acquisition function to find multiple global and local optimal regions, avoiding the tendency to becoming trapped in a single optimum. To distinguish between a true and false optimal region due to noisy experimental measurements, a human (domain) knowledge driven dynamic surrogate gate is integrated with SANE. We implemented the gate-SANE into pre-acquired piezoresponse spectroscopy data of a ferroelectric combinatorial library with high noise levels in specific regions, and piezoresponse force microscopy (PFM) hyperspectral data. SANE demonstrated better performance than classical BO to facilitate the exploration of multiple optimal regions and thereby prioritized learning with higher coverage of scientific values in autonomous experiments. Our work showcases the potential application of this method to real-world experiments, where such combined strategic and human intervening approaches can be critical to unlocking new discoveries in autonomous research.

Biswas, Arpan [University of Tennessee, Knoxville,↗

DOE OSTI2025

Causal discovery from data assisted by large language models

Knowledge-driven discovery of novel materials necessitates the development of causal models for property emergence. While in the classical physical paradigm, the causal relationships are deduced based on physical principles or via experiment, the rapid accumulation of observational data necessitates learning causal relationships between dissimilar aspects of material structure and functionalities based on observations. For this, it is essential to integrate experimental data with prior domain knowledge. Here, we demonstrate this approach by combining high-resolution scanning transmission electron microscopy data with insights derived from large language models (LLMs). By applying ChatGPT to domain-specific literature, such as arXiv papers on ferroelectrics, and combining the obtained information with data-driven causal discovery, we construct adjacency matrices for directed acyclic graphs that map the causal relationships between structural, chemical, and polarization degrees of freedom in Sm-doped BiFeO 3 . This approach enables us to hypothesize how synthesis conditions influence material properties and guides experimental validation. Furthermore, the ultimate objective of this work is to develop a unified framework that integrates LLM-driven literature analysis with data-driven discovery, facilitating the precise engineering of ferroelectric materials by establishing clear connections between synthesis conditions and their resulting material properties.

Causal inference↗

DOE OSTI2025

Combining MicroED and native mass spectrometry for structural discovery of enzyme–small molecule complexes

With the goal of accelerating the discovery of small molecule–protein complexes, we leverage fast, low-dose, event-based electron counting microcrystal electron diffraction (MicroED) data collection and native mass spectrometry. This approach, which we term electron diffraction with native mass spectrometry (ED-MS), allows assignment of protein target structures bound to ligands with data obtained from crystal slurries soaked with mixtures of known inhibitors and crude biosynthetic reactions. This extends to libraries of printed ligands dispensed directly onto TEM grids for later soaking with microcrystal slurries, and complexes with noncovalent ligands. ED-MS resolves structures of the natural product, epoxide-based cysteine protease inhibitor E-64, and its biosynthetic analogs bound to the model cysteine protease, papain. It further identifies papain binding to its preferred natural products, by showing that two analogs of E-64 outcompete others in binding to papain crystals, and by detecting papain bound to E-64 and an analog from crude biosynthetic reactions, without purification. ED-MS also resolves binding of the CTX-M-14 β-lactamase, a target of active drug development, to the non-β-lactam inhibitor, avibactam, alone or in a cocktail of unrelated compounds. These results illustrate the utility of ED-MS for natural product ligand discovery and for structure-based screening of small molecule binders to macromolecular targets, promising utility for drug discovery.

MicroED↗

DOE OSTI2025

mDNS to support local price server discovery with OpenADR 3 (mDNS for OpenADR 3) v1.0

This software contains a template VEN with local VTN service discovery over mDNS. It provides common starter code for an OpenADR3.0 VEN that advertises itself over mDNS, conducts local VTN service discovery over mDNS, connects to the VTN over HTTP(S), and regularly polls and acts on energy prices and events hosted on the VTN. The software is written to be easily modified to accommodate different VEN appliances, VEN-VTN networking protocols, user interfaces, and default responses, given the wide range of possible use cases for local price server discovery. OpenADR3.0 is an open communications standard from the OpenADR Alliance that is designed to provide two-way information exchange regarding e.g., dynamic price and event signals to utility applications, so that customers can modify their energy usage to save money and reduce their carbon footprint.

Nordman, Bruce [Lawrence Berkeley National Laborat↗

DOE OSTI2024

Discovery Science and Inertial Fusion Energy Research at the Jupiter Laser Facility (Research Performance Progress Report)

The goal of this project is to provide operational support to run the Jupiter Laser Facility within the LaserNetUS network to achieve the following four objectives: • Develop new science, techniques, and platforms for discovery science and IFE research, in partnership with academia, other LaserNetUS nodes, and the greater community. • Advance the development of secondary sources of photons and particles for applications relevant to discovery science and IFE; • Serve as a testbed for new laser, optical, target, and diagnostic capabilities that will advance IFE; • Attract, train, and retain talent in high-energy-density and laser science that will be essential in furthering development of IFE, and help build new collaborations between national laboratory and academic researchers. We have accomplished our four objectives by: • Providing access to the three JLF platforms (Titan, Janus, and COMET) to LaserNetUS users after their proposals have been independently reviewed and ranked by the LaserNetUS PRP; • Providing expertise and technical capabilities to support focused science research thrusts at the facility; • Promoting and maintaining technical relationships and collaborations with other members of the LaserNetUS community to nurture and grow the discovery science and IFE workforce— especially students and early career scientists—on LaserNetUS facilities. • Augmenting JLF with specific improvements while coordinating efforts with LLNL organizations and collaborators to provide users with optimal laser, target, and diagnostic resources to help them maximize technical impact.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2024

A goldilocks computational protocol for inhibitor discovery targeting DNA damage responses including replication-repair functions

While many researchers can design knockdown and knockout methodologies to remove a gene product, this is mainly untrue for new chemical inhibitor designs that empower multifunctional DNA Damage Response (DDR) networks. Here, we present a robust Goldilocks (GL) computational discovery protocol to efficiently innovate inhibitor tools and preclinical drug candidates for cellular and structural biologists without requiring extensive virtual screen (VS) and chemical synthesis expertise. By computationally targeting DDR replication and repair proteins, we exemplify the identification of DDR target sites and compounds to probe cancer biology. Our GL pipeline integrates experimental and predicted structures to efficiently discover leads, allowing early-structure and early-testing (ESET) experiments by many laboratories. By employing an efficient VS protocol to examine protein-protein interfaces (PPIs) and allosteric interactions, we identify ligand binding sites beyond active sites, leveraging in silico advances for molecular docking and modeling to screen PPIs and multiple targets. A diverse 3,174 compound ESET library combines Diamond Light Source DSI-poised, Protein Data Bank fragments, and FDA-approved drugs to span relevant chemotypes and facilitate downstream hit evaluation efficiency for academic laboratories. Two VS per library and multiple ranked ligand binding poses enable target testing for several DDR targets. This GL library and protocol can thus strategically probe multiple DDR network targets and identify readily available compounds for early structural and activity testing to overcome bottlenecks that can limit timely breakthrough drug discoveries. By testing accessible compounds to dissect multi-functional DDRs and suggesting inhibitor mechanisms from initial docking, the GL approach may enable more groups to help accelerate discovery, suggest new sites and compounds for challenging targets including emerging biothreats and advance cancer biology for future precision medicine clinical trials.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Lightcurves, Rotation Periods, and Colors for Vera C. Rubin Observatory’s First Asteroid Discoveries

We present lightcurves, rotation periods, and colors for the first asteroid discoveries made with the NSF-DOE Vera C. Rubin Observatory. These are the first science results derived from the 2103 asteroid discoveries released as part of the Rubin First Look (RFL) media event on 2025 June 23, in which the first LSST Camera commissioning images were released. The ∼340,000 observations in which the discoveries were made span nine nights between 2025 April 21 and May 5. With a limiting single-epoch 5σ depth of ∼23–25 mag and dense temporal sampling under an irregular, commissioning-driven cadence, the RFL observations provide an ideal test bed for determination of rotation periods, including sensitivity to rapid rotation. We model lightcurves and derive rotation periods and colors for the ∼2000 objects. We find 75 main-belt asteroids (MBAs) and one near-Earth object (NEO) with reliable rotation periods spanning 0.031–21.3 hr and a photometric precision in the range of 0.05–0.15 mag. We find 19 superfast rotators with periods shorter than the 2.2 hr spin barrier. Rubin-discovered MBA 2025 MN 45 is the fastest-rotating d > 0.5 km known asteroid with a rotation period of 1.9 minutes; along with NEO 2025 MJ 71 (1.9 minutes) and Rubin-discovered MBAs 2025 MK 41 (3.8 minutes), 2025 MV 71 (13 minutes), and 2025 MG 56 (16 minutes), these five super- to ultrafast rotators join a couple of NEOs as the fastest-spinning subkilometer asteroids known. As this study demonstrates, even in early commissioning, Rubin is successfully probing a previously sparsely sampled region of the subkilometer size−spin rate regime for MBAs.

Greenstreet, Sarah [NSF National Optical-Infrared ↗

NASA NTRS1983

The discovery circumstances of Earth-approaching asteroids

The discovery circumstances are analyzed for all Earth-approaching asteroids detected in the last twenty-four years. In particular, topocentric angular velocities, opposition distance, geocentric and heliocentric distances, phase angle, and lunar phase at discover were calculated in an effort to separate any selection effects between chance and purposeful (i.e., as the result of a systematic search) discoveries. Another motivation was the possibility of discerning useful clues how to search more efficiently for such objects. There are 60 minor planets in the sample. The principal result is that the discovery of Earth-approaching asteroids is dominated by serendipity. Therefore, searching for them at the current relatively bright limits at less than a very high rate seems pointless.

Taff, L. G.↗

NASA NTRS1985

Discovery of a probable galaxy with a redshift of 3.218

The discovery of a narrow emission line object, probably a galaxy, with a redshift of 3.218, is reported. The object is a companion to the quasar PKS 1614 + 051, which is at a redshift of 3.209. This is the most distant non-QSO, nongravitationally lensed object presently known by a large margin. Its properties are consistent with those expected of a high-redshift galaxy. This object has an age of only a few percent of the present age of the universe. The object was discovered with a novel technique, which promises to push studies of distant galaxies to redshifts as high as those of the most distant quasars known, and which may eventually lead to the discovery of primeval galaxies. This discovery opens the way for studies of galaxies beyond redshift three, which should prove invaluable for observational cosmology.

Djorgovski, S.↗

NASA NTRS1991

Discovery and orbital characterization of near-Earth asteroids

The fundamentals of photographic discovery are discussed, and the work at the Palomar Observatory is described including photographic discovery programs elsewhere. The Spacewatch development of CCD-scanning techniques is reviewed. Special searches for objects near the Earth are reported. The existence of four streams among both Earth-approaching asteroids and meteorite-dropping fireballs suggests that at certain times of the year an increase can be expected in both asteroid discoveries and meteoritic events.

Gehrels, T.↗

NASA NTRS1995

Workshop on Discovery Lessons-Learned

As part of the Discovery Program's continuous improvement effort, a Discovery Program Lessons-Learned workshop was designed to review how well the Discovery Program is moving toward its goal of providing low-cost research opportunities to the planetary science community while ensuring continued U.S. leadership in solar system exploration. The principal focus of the workshop was on the recently completed Announcement of Opportunity (AO) cycle, but the program direction and program management were also open to comment. The objective of the workshop was to identify both the strengths and weaknesses of the process up to this point, with the goal of improving the process for the next AO cycle. The process for initializing the workshop was to solicit comments from the communities involved in the program and to use the feedback as the basis for establishing the workshop agenda. The following four sessions were developed after reviewing and synthesizing both the formal feedback received and informal feedback obtained during discussions with various participants: (1) Science and Return on Investment; (2) Technology vs. Risk; Mission Success and Other Factors; (3) Cost; and (4) AO.AO Process Changes and Program Management.

Saunders, M.↗

NASA NTRS2001

Searching the ASRS Database Using QUORUM Keyword Search, Phrase Search, Phrase Generation, and Phrase Discovery

To support Search Requests and Quick Responses at the Aviation Safety Reporting System (ASRS), four new QUORUM methods have been developed: keyword search, phrase search, phrase generation, and phrase discovery. These methods build upon the core QUORUM methods of text analysis, modeling, and relevance-ranking. QUORUM keyword search retrieves ASRS incident narratives that contain one or more user-specified keywords in typical or selected contexts, and ranks the narratives on their relevance to the keywords in context. QUORUM phrase search retrieves narratives that contain one or more user-specified phrases, and ranks the narratives on their relevance to the phrases. QUORUM phrase generation produces a list of phrases from the ASRS database that contain a user-specified word or phrase. QUORUM phrase discovery finds phrases that are related to topics of interest. Phrase generation and phrase discovery are particularly useful for finding query phrases for input to QUORUM phrase search. The presentation of the new QUORUM methods includes: a brief review of the underlying core QUORUM methods; an overview of the new methods; numerous, concrete examples of ASRS database searches using the new methods; discussion of related methods; and, in the appendices, detailed descriptions of the new methods.

McGreevy, Michael W.↗

NASA NTRS2001

The Discovery of a Second Luminous Low Mass X-Ray Binary System in the Globular Cluster M15

Using the Chandra X-ray Observatory we have discovered a second bright X-ray source in the globular cluster M15 that is 2.7" to the west of AC211, the previously known low mass X-ray binary (LMXB) in this system. Prior to the 0.5" imaging capability of Chandra this second source could not have been resolved from AC211. The luminosity and spectrum of this new source, which we call M15-X2, are consistent with it also being a LMXB system. This is the first time that two LMXBs have been seen to be simultaneously active in a globular cluster. The new source, M15-X2, is coincident with a 18th U magnitude very blue star. The discovery of a second LMXB in M15 clears up a long standing puzzle where the X-ray and optical properties of AC211 appear consistent with the central source being hidden behind an accretion disk corona, and yet also showed a luminous X-ray burst suggesting the neutron star is directly visible. This discovery suggests instead that the X-ray burst did not come from AC211, but rather from the newly discovered X-ray source. We discuss the implications of this discovery for X-ray observations of globular clusters in nearby galaxies.

White, Nicholas E.↗

NASA NTRS2000

STS-92 Meal - Suit up - Depart O&C - Launch Discovery On Orbit - Landing - Crew Egress

The video begins with the introduction of the crew of Space Shuttle Discovery on STS-92, at their customary pre-flight meal. The crew consists of Commander Brian Duffy, Pilot Pamela Melroy, and Mission Specialists Leroy Chiao, William McArthur, Peter "Jeff" Wisoff, Michael Lopez-Alegria, and Koichi Wakata. The introduction and suit-up of the astronauts, and their departure in the Astrovan are shown at a quick pace. The video shows in detail the seating of the crew and each astronaut's final preparations in the White Room prior to boarding. Views of Discovery's night launch include: SLF Convoy, Beach Tracker, VAB, Pad Perimeter, Tower-1, UCS-15, Press Site, UCS-23, OTV-61, OTV-70, OTV-71, and the In-Cabin Ascent Camera. While in orbit, the Discovery orbiter docks with the International Space Station (ISS). The docking is shown in a series of still images. The video includes clips from four extravehicular activities (EVAs). The crew members who performed the EVAs comment on them while speaking to Mission Control. During the EVAs, the Z1 Truss and an antenna are attached to the ISS. The crew members on the fourth EVA test jet packs. Views of landing include: TV-1, TV-2, TV-3, LRO-1, and HUD.

Source record↗

NASA NTRS2001

STS-103 Photo-op/Suit-up/Depart O&C/Launch Discovery On-Orbit/Landing/Crew Egress

The crew of the STS-103 space mission are shown as they prepare for launch and landing of the space shuttle discovery. The crew includes: Commander Curtis L. Brown, Pilot Scott J. Kelly, and Mission Specialists: Steven L. Smith, C. Michael Foale, John M. Grunsfeld, Claude Nicollier and Jean-francois Clervoy. Footage of these astronauts during suit-up, Ingress, Egress and Operations and Checkout (O&C) is presented. Live footage of the countdown and launch of the space shuttle discovery is shown from various vantage points such as the Tower 1, Vehicle Assembly Building (VAB), and pad perimeter. Once in orbit, a presentation of Steven Smith, John Grunsfield, Michael Foale and Claude Nicollier performing three spacewalks to repair the HST is shown. The landing of the space shuttle discovery at the Kenndy Space Center is shown.

Source record↗

NASA NTRS2005

STS-114: Discovery Impromptu Briefing

Dr. Griffin, NASA Administrator, is accompanied by members of The U.S. House of Representatives in this STS-114 Discovery Impromptu briefing. The U.S. House of Representatives present include: Sherwood Boehlert, House Science Committee Chairman, Senator Hutchinson, Sheila Jackson, 18th Congressional District Texas, Al Green, 9th Congressional District, Representative Jim Davis, Florida, and Gene Green, 29th District, Texas. Griffin talks about the problem that occurred with the external fuel tank sensor of the Space Shuttle Discovery and the effort NASA is pursuing to track the problem, and identify the root cause. He answers questions from the news media about the next steps for the Space Shuttle Discovery, time frame for the launch, and activities for the astronauts for the next few days.

Source record↗

NASA NTRS2005

The Challenges of Interoperable Data Discovery

The Global Change Master Directory (GCMD) assists the oceanographic community in data discovery and access through its online metadata directory. The directory also offers data holders a means to post and search their oceanographic data through the GCMD portals, i.e. online customized subset metadata directories. The Gulf of Maine Ocean Data Partnership (GoMODP) has expressed interest in using the GCMD portals to increase the visibility of their data holding throughout the Gulf of Maine region and beyond. The purpose of the Gulf of Maine Ocean Data Partnership (GoMODP) is to "promote and coordinate the sharing, linking, electronic dissemination, and use of data on the Gulf of Maine region". The participants have decided that a "coordinated effort is needed to enable users throughout the Gulf of Maine region and beyond to discover and put to use the vast and growing quantities of data in their respective databases". GoMODP members have invited the GCMD to discuss further collaborations in view of this effort. This presentation. will focus on the GCMD GoMODP Portal - demonstrating its content and use for data discovery, and will discuss the challenges of interoperable data discovery. interoperability among metadata standards and vocabularies will be discussed. A short overview of the lessons learned at the Marine Metadata Interoperability (MMI) metadata workshop held in Boulder, Colorado on August 9-11, 2005 will be given.

Meaux, Melanie F.↗