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opencc-by-4.0Oct 2022View details →

PanDDA files from a ligand screen against the NSP3 macrodomain of SARS-CoV-2 - ligands from linking with FRESCO

This deposition contains the X-ray diffraction data used to run PanDDA in the ligand screen against the NSP3 macrodomain of SARS-CoV-2 described in McCorkindale et al. 2022 (https://doi.org/10.1101/2022.11.21.517375). mac1_pandda.zip contains the structure factor intensities, PanDDA input/ouput and refined models/maps. A description of the files can be found in the README file.  mac1_ligand-bound_states.zip contains the ligand-bound states extracted from the multi-state PDB files.

opencc-by-4.0Dec 2022View details →

Data snapshot from the Protein Ligand Binding Database (PLBD)

Data snapshot from the Protein Ligand Binding Database (PLBD) ============================================================= This data set contains tabular data snapshots from the PLBD. Data are provided in the time-stamped JSON [1] files. The time stamp in all files (the first line of each data file) records the moment when the data tables were retrieved from the PLBD server. Since the PLBD is a constantly evolving database, it is recommended that the latest data from the PLBD server [2] are downloaded and used, unless historic data are needed. The provided Makefile illustrates a possible download procedure. The tables here are provided solely to comply with the editorial policies of the "Scientific Data" journal. The ".json" files in the "outputs/main" directory contain the data; the ".nrec" files contain the number of records in the PLBD tables at the moment of download (a single decimal integer recorded on the second line of each ".nrec" file) and were used to request the the appropriate number of rows when downloading the "outputs/main/*.json" files. The meaning and the data type descriptions of the JSON file attributes are provided in the database description file "main-database-description.xml". This file is deposited as a separate digital object in Zenodo [3]. The layout of the JSON files follows ideas described in the JSON:API schema [4]. Layout of the archived file tree --------------------------------     .     ├── Makefile     ├── README     ├── README.pdf     ├── inputs     │   ├── tables.lst     │   ├── tables.lst.history     │   └── tables.lst.log     ├── makefiles     │   ├── available     │   │   ├── Makelocal-download-json     │   │   └── Makelocal-download-nrec     │   └── enabled     │       ├── Makelocal-download-json     │       └── Makelocal-download-nrec     └── outputs         └── main [52 entries exceeds filelimit, not opening dir] References: 1. ECMA Standard. The JSON data interchange syntax. 2017, 1-16, URL: https://www.ecma-international.org/publications/files/ECMA-ST/ECMA-404.pdf 2. The Protein Ligand Binding Database (PLBD) server. URL: https://plbd.org/db/main [accessed: 2022-12-21T09:29+02:00] 3. Lingė, D.; Gedgaudas, M.; Merkys, A.; Petrauskas, V.; Vaitkus, A.; Grybauskas, A.; Paketurytė, V.; Zubrienė, A.; Zak&scaron;auskas, A.; Mickevičiūtė, A.; Smirnovienė, J.; Baranauskienė, L.; Čapkauskaitė, E.; Dudutienė, V.; Urniežius, E.; Konovalovas, A.; Kazlauskas, E.; Gražulis, S. & Matulis, D. PLBD (Protein Ligand Binding Database) table description XML file. Zenodo, 2022, DOI: https://doi.org/10.5281/ZENODO.7482008 4. Katz, Y.; Gebhardt, D.; Sullice, G.; Hanschke, J.; Kellen, T.; Klabnik, S. & Resnick, E. JSON:API version 1.1. 2022 URL: https://jsonapi.org/format/1.1/ [accessed: 2022-12-25T16:04+02:00]

opencc-by-4.0Jan 2023View details →

Data: Complementary Experimental Methods to Obtain Thermodynamic Parameters of Protein Ligand Systems

Data, which are presented in the following publication: Mohanakumar, Shilpa; Lee, Namkyu; Wiegand, Simone (2022): Complementary Experimental Methods to Obtain Thermodynamic Parameters of Protein Ligand Systems. In: International Journal of Molecular Sciences 23 (22), S. 14198. DOI: 10.3390/ijms232214198.

dryad32/100

Characterizing the consensus residue specificity and surface of Bcl-2 binding to BH3 ligands using the knob-socket model

Cancer cells bypass cell death by changing the expression of the BCL-2 family of proteins, which are apoptotic pathway regulators. Upregulation of pro-survival BCL-2 proteins or downregulation of cell death effectors BAX and BAK interferes with the initiation of the intrinsic apoptotic pathway. In normal cells, apoptosis can occur through pro-apoptotic BH3-only proteins interacting and inhibiting pro-survival BCL-2 proteins. When cancer cells over-express pro-survival BCL-2 proteins, a potential remedy is the sequestration of these pro-survival proteins through a class of anti-cancer drugs called BH3 mimetics that bind in the hydrophobic groove of pro-survival BCL-2 proteins. To improve the design of these BH3 mimetics, the packing interface between BH3 domain ligands and pro-survival BCL-2 proteins was analyzed using the Knob-Socket model to identify the amino acid residues responsible for interaction affinity and specificity. A Knob-Socket analysis organizes all the residues in a binding interface into simple 4 residue units: 3-residue sockets defining surfaces on a protein that pack a 4th residue knob from the other protein. In this way, the position and composition of the knobs packing into sockets across the BH3/BCL-2 interface can be classified. A Knob-Socket analysis of 19 BCL-2 protein and BH3 helix co-crystals reveal multiple conserved binding patterns across protein paralogs. Conserved knob residues such as a Gly, Leu, Ala and Glu most likely define binding specificity in the BH3/BCL-2 interface, whereas other residues such as Asp, Asn, and Val are important for forming surface sockets that bind these knobs. These findings can be used to inform the design of BH3 mimetics that are specific to pro-survival BCL-2 proteins for cancer therapeutics.

opencc-zeroJan 2023View details →

opencc-by-4.0Jul 2021View details →

Load-bearing hydrogels ionically reinforced through competitive ligand exchanges

Fast advances in soft robotics and tissue engineering demand for new soft materials whose mechanical properties can be interchangeably and locally varied, thereby enabling, for example, the design of soft joints within an integral material. Inspired by nature, we introduce a competitive ligand-mediated approach to selectively and interchangeably reinforce metal-coordinated hydrogels. This is achieved by reinforcing carboxylate-containing hydrogels with Fe3+ ions. Key to achieving a homogeneous, predictable reinforcement of the hydrogels is the presence of weak complexation agents that delay the formation of metal-complexes within the hydrogels, thereby allowing a homogeneous distribution of the metal ions. The resulting metal-reinforced hydrogels show a compressive modulus of up to 2.5 MPa, while being able to withstand pressures as high as 0.6 MPa without appreciable damage. Competitive ligand exchanges offer an additional advantage: they enable non-linear compositional changes that, for example, allow the formation of joints within these hydrogels. These features open up new possibilities to extend the field of use of metal reinforced hydrogels to load-bearing applications that are omnipresent for example in soft robots and actuators.

opencc-by-4.0Dec 2022View details →

Proteome-wide structure-based accessibility analysis of ligandable and detectable cysteines in chemoproteomic datasets

Covalent drug discovery, in particular targeting reactive cysteines, has undergone a resurgence over the past two decades, demonstrated by recent clinical successes of covalent inhibitors for high-priority cancer targets. Reactive cysteine profiling, first pioneered by the Cravatt lab, has emerged in parallel as a powerful approach for proteome-wide on- and off-target profiling. Thus far however, structural analysis of liganded cysteines has been restricted to experimentally determined protein structures. We combined AlphaFold-predicted amino acid side chain accessibilities for >95% of the human proteome with a meta-analysis of thirteen public cysteine profiling datasets, totalling 40,070 unique cysteine residues, revealing accessibility biases in sampled cysteines primarily dictated by warhead chemistry. Analysis of >3.5 million cysteine-fragment interactions further suggests that exposed cysteine residues are preferentially targeted by elaborated fragments and drug-like compounds. We finally propose a framework for benchmarking coverage of ligandable cysteines in future cysteine profiling approaches, considering both selectivity for high-priority residues and quantitative depth. All analysis and produced resources (freely available at <a href="http://www.github.com/TateLab">www.github.com/TateLab</a>) are readily extendable to reactive amino acids beyond cysteine, and related questions in chemical biology.

opencc-by-4.0Jun 2023View details →

DOX_BDW: Incorporating Solvation and Desolvation Effects of Cavity Water into Nonfitting Protein–Ligand Binding Affinity Prediction

structures.zip:  including the coordinates of all optimized proteinligand complex structure obtained by DOX_BDW calculation. (compressed PDB file). These pdb files could also be  used as input for the binding energy calculation,as illustrated in SI section 8.  mdinput.zip: Including the input files,parameter files, topology files needed to run MD simulation for water mapping, as illustrated in SI section 8. Note that all of the parameter files and topology files would be automatically generated using the RUNMD program we uploaded with the example file.  example.zip: The programs and input files needed to run an example, as illustrated in SI section 9. And all the output files except MD trajectories are in there,too.

opennotspecifiedFeb 2022View details →

Fig. 6. Overlapped top-scored poses for ligands 19 in Monoterpene indole alkaloids from Vinca minor L. (Apocynaceae): Identification of new structural scaffold for treatment of Alzheimer's disease

Fig. 6. Overlapped top-scored poses for ligands 19 (blue) and crystal structure of tacrine (green) in the active site of hBuChE (PDB ID: 4BDS). Amino acid residues involved in the interactions with ligands are depicted as either grey or yellow (catalytic triad) lines. The rest of the receptor is displayed in light-grey cartoon conformation. The Figure was created with The PyMOL Molecular Graphics System, Version 2.4.1, Schr¨odinger, LLC. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

opennotspecifiedMay 2020View details →

Fig. 4 in Benzofuran and coumarin derivatives from the root of Angelica dahurica and their PPAR-γ ligand-binding activity

Fig. 4. PPAR-γ ligand binding activity of 1–21. Pioglitazone (PG): 50 (■) and 5.0 (□) μM, 1–21: 500 and 50 μM. Data are represented as the mean ± S.E.M. (n = 3). Dunnett's test was used for statistical analysis. ***p <0.001, **p <0.01, *p <0.05.

opencc-by-4.0Dec 2022View details →

Dataset for "Structure and Properties of Metallosupramolecular Polymers with a Nitrogen-Based Bidentate Ligand"

Source data of the study reported in the publication entitled "Structure and Properties of Metallosupramolecular Polymers with a Nitrogen-Based Bidentate Ligand". The data should be considered together with the published manuscript and the supplementary information file.

opencc-by-4.0Sep 2023View details →

Unexpected Latency of Z-Stereoretentive Ruthenium Olefin Metathesis Catalysts Bearing Unsymmetrical N-heterocyclic Carbene or Cyclic(alkyl)(amino)carbene Ligands

Data confirming the structure of the new compounds obtained within the project, published in Organometallics 2023, 42, 2453–2459; <a href="https://doi.org/10.1021/acs.organomet.2c00428">doi.org/10.1021/acs.organomet.2c00428</a> The research was supported by the National Science Centre, Poland (OPUS grant 2019/33/B/ST4/00874).

opencc-by-4.0Dec 2023View details →

Dataset to Carbon nanotube field-effect transistor for resolving single-molecule aptamer-ligand binding kinetics

Raw data of single molecular field effect transistor data from recordings of aptamer serotonin interactions.

A Phase I Study of a DNA Vaccine Encoding Androgen Receptor Ligand-Binding Domain (AR LBD) +/-GMCSF

ClinicalTrials.gov study NCT02411786. IPD Sharing: Not stated. Countries: 1. Publications: 1.

Adoptive Immunotherapy of High Risk Acute Myeloblastic Leukemia Patients Using Haploidentical Kir Ligand-mismatched Natural Killer Cells

ClinicalTrials.gov study NCT00799799. IPD Sharing: Not stated. Countries: 1. Publications: 2.

A Study of Atezolizumab (an Engineered Anti-Programmed Death-Ligand 1 [PDL1] Antibody) to Evaluate Safety, Tolerability and Pharmacokinetics in Participants With Locally Advanced or Metastatic Solid T

ClinicalTrials.gov study NCT01375842. IPD Sharing: Not stated. Countries: 4. Publications: 14.

A Study of TACI（Transmembrane Activator and Calcium-modulator and Cyclophilin Ligand (CAML) Interactor）-Antibody Fusion Protein Injection (RC18) in Subjects With Systemic Myasthenia Gravis

ClinicalTrials.gov study NCT04302103. IPD Sharing: Not stated. Countries: 1. Publications: 0.

controlledIPD-YESFeb 2026View details →

A Novel 68Ga Labeled FAP Ligand PET/CT in Patients With Various Malignant Tumors

ClinicalTrials.gov study NCT06186427. IPD Sharing: YES. Countries: 1. Publications: 3.

closedIPD-NOFeb 2026View details →

Radiation Dosimetry of the 18 kDa Translocator Protein Ligand [18F]PBR111 in Humans

ClinicalTrials.gov study NCT06398392. IPD Sharing: NO. Countries: 1. Publications: 1.

A Study of Atezolizumab (Anti-Programmed Death-Ligand 1 [PD-L1] Antibody) Alone or in Combination With an Immunomodulatory Drug and/or Daratumumab in Participants With Multiple Myeloma (MM)

ClinicalTrials.gov study NCT02431208. IPD Sharing: Not stated. Countries: 1. Publications: 1.

PET Whole Body Imaging Using a Peripheral Benzodiazepine Receptor Ligand [C-11]PBR28

ClinicalTrials.gov study NCT00407693. IPD Sharing: Not stated. Countries: 1. Publications: 3.