cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5517/ccdc.csd.cc2k513x
title: CCDC 2358328: Experimental Crystal Structure Determination

description: Related Article: M. Dailey, E.W. Jackson, T.R. Ramadhar|2024|Acta Crystallogr.,Sect.C:Cryst.Struct.Chem.|80|545|doi:10.1107/S205322962400737X
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2kn8vc
title: CCDC 2372983: Experimental Crystal Structure Determination

description: Related Article: C.B. Pinto, L.H.R. Dos Santos, B.L. Rodrigues|2024|Acta Crystallogr.,Sect.C:Cryst.Struct.Chem.|80|478|doi:10.1107/S2053229624007125
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2kq17l
title: CCDC 2374669: Experimental Crystal Structure Determination

description: Related Article: J.-T. Wu, L. Song, W.-Z. Xu, X.-Y. Wei, Y.-X. Zhang, Y.-Y. Zhang, X.-Y. Du, W.-X. Chai|2024|Acta Crystallogr.,Sect.C:Cryst.Struct.Chem.|80|538|doi:10.1107/S2053229624006983
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2kqy8j
title: CCDC 2375538: Experimental Crystal Structure Determination

description: Related Article: E. Bosch, N.P. Bowling|2024|Acta Crystallogr.,Sect.C:Cryst.Struct.Chem.|80|553|doi:10.1107/S205322962400771X
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2kqy9k
title: CCDC 2375539: Experimental Crystal Structure Determination

description: Related Article: E. Bosch, N.P. Bowling|2024|Acta Crystallogr.,Sect.C:Cryst.Struct.Chem.|80|553|doi:10.1107/S205322962400771X
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2kqybl
title: CCDC 2375540: Experimental Crystal Structure Determination

description: Related Article: E. Bosch, N.P. Bowling|2024|Acta Crystallogr.,Sect.C:Cryst.Struct.Chem.|80|553|doi:10.1107/S205322962400771X
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2kqycm
title: CCDC 2375541: Experimental Crystal Structure Determination

description: Related Article: E. Bosch, N.P. Bowling|2024|Acta Crystallogr.,Sect.C:Cryst.Struct.Chem.|80|553|doi:10.1107/S205322962400771X
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2k5924
title: CCDC 2358575: Experimental Crystal Structure Determination

description: Related Article: R. Atencio, M.M. Linares, T. González, A. Briceño|2024|Acta Crystallogr.,Sect.C:Cryst.Struct.Chem.|80|487|doi:10.1107/S2053229624007897
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2k5935
title: CCDC 2358576: Experimental Crystal Structure Determination

description: Related Article: R. Atencio, M.M. Linares, T. González, A. Briceño|2024|Acta Crystallogr.,Sect.C:Cryst.Struct.Chem.|80|487|doi:10.1107/S2053229624007897
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2k5946
title: CCDC 2358577: Experimental Crystal Structure Determination

description: Related Article: R. Atencio, M.M. Linares, T. González, A. Briceño|2024|Acta Crystallogr.,Sect.C:Cryst.Struct.Chem.|80|487|doi:10.1107/S2053229624007897
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2k5957
title: CCDC 2358578: Experimental Crystal Structure Determination

description: Related Article: R. Atencio, M.M. Linares, T. González, A. Briceño|2024|Acta Crystallogr.,Sect.C:Cryst.Struct.Chem.|80|487|doi:10.1107/S2053229624007897
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.25666/dataubfc-2023-07-17
title: 4’-(N-(2-cyanoethyl)pyrrol-2-yl)-2,2’:6’,2’’-terpyridine
title: 4’-(N-(2-cyanoethyl)pyrrol-2-yl)-2,2’:6’,2’’-terpyridine

description: Data for the synthesis and caracterization of 4’-(N-(2-cyanoethyl)pyrrol-2-yl)-2,2’:6’,2’’-terpyridine.
description: Données pour la synthèse et la caractérisation du composé 4’-(N-(2-cyanoethyl)pyrrol-2-yl)-2,2’:6’,2’’-terpyridine.
description: Audience: University: master, Research, University: licence
description: UpdatePeriodicity: no update
description: Project: FINEAU – FIbres Naturelles pour le traitement des EAUx, Région Bourgogne-Franche-Comté 2020 (Region Bourgogne Franche-Comté)
description: Project: Recyclage de boues d’hydroxydes d’aluminium en catalyseurs, SRO OSU THETA 2022 (OSU)
description: Label: PCU UTINAM (Plateforme de chimie UTINAM PCU)
description: Experimental data: NMR; IR; HRMS
description: Données expérimentales: RMN; IR; HRMS
DOI: 10.34740/kaggle/dsv/9275054
title: Trending Youtube Video Statistics (113 Countries)
DOI: 10.15468/dl.rqjs86
title: Occurrence Download

description: A dataset containing 340016 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Scolopax rusticola Linnaeus, 1758",
 "HasCoordinate is true",
 "Year is greater than or equal to 2011",
 "Year is less than or equal to 2024"
 ]
}

 The dataset includes 340016 records from 942 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0107771-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.13490047
title: Impact of intangible assets on financial performance of companies in Georgia
DOI: 10.5281/zenodo.13490048
title: Impact of intangible assets on financial performance of companies in Georgia
DOI: 10.15468/dl.wans3s
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Theages hoffmani Travassos, 1962"
 ]
}

 The dataset includes 6 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0107774-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.b4zyrg
title: Occurrence Download

description: A dataset containing 810 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Colombia",
 "TaxonKey is Rhinella alata (Thominot, 1884)"
 ]
}

 The dataset includes 810 records from 40 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0107775-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mv7322
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-71.7914 -33.18206,-70.95944 -33.18206,-70.95944 -32.86245,-71.7914 -32.86245,-71.7914 -33.18206))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Leucocoryne foetida Phil."
 ]
}

 The dataset includes 5 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0107777-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.11121884
title: Data and code for, "Large language models design sequence-defined macromolecules via evolutionary optimization"

description: # Codes and data for "Large language models design sequence-defined macromolecules via evolutionary optimization"Note this repository contains codes and data files for the manuscript. This is a snapshot of the repository, frozen at the time of submission.# Codes## LLM codes- `run_claude.py` - the routine for performing LLM-based rollouts; intended for command line execution using argparse- `message_utils.py` - utilities for constructing and parsing messages for LLM I/O- `model_utils.py` - lightweight utilities for retrieving formatted predictions from the RNN ensemble- `target_defs.py` - defines the sequence, locations, and natural language descriptions of the target structures- `ask_about_oracle.ipynb` - asks the LLM to speculate about the nature of the optimization task## other algorithms- `active_learning.ipynb` - use EI acquisition with RF surrogate to label new sequences; includes an unused tokenization scheme- `evolutionary_algorithm.ipynb` - use DEAP library to perform evolutionary optimization- `random_sampling.ipynb` - sample sequences randomly from all possible sequences## postprocessing- `process_aggregated_logs.py` - reads data from the raw log files and prepares them for visualization- `process_sample_rollouts.py` - reads data from the raw log files and prepares individual rollouts## visualization- `figure1b.ipynb` - renders panel b of Fig. 1- `figure1efg.ipynb` - renders the last row of Fig. 1 (panels e-g)- `figure2.ipynb` - renders all of Fig. 2- `figure_si.ipynb` - renders Figs. S1 and S2- `figure_md_validation.ipynb` - renders Fig. S3# Data files- `prompts/`  - `prompt-scientific-v4.4.yml` - the full text of the scientific prompt, to be read by `run_claude.py`  - `prompt-oracle-v4.4.yml` - the full text of the oracle prompt, to be read by `run_claude.py`- `models/` - the TorchScript RNN models used to make predictions- `data/`  - `embeddings` - calculated embeddings for a collection of sequences from our prior work  - `llm-logs` - the raw logs obtained from the Claude 3.5 Sonnet LLM (other algorithms made to look like the LLM logs after the fact)  - `llm-logs-opus` - the raw logs obtained from the Claude 3.0 Opus LLM (used in the first draft of the article, replaced by Claude 3.5 Sonnet)   - `all-rollouts-kltd.csv` - postprocessed logs for all the rollouts using the "top $k < d^*$" metric  - `all-rollouts-topkd.csv` - postprocessed logs for all the rollouts using the "mean $d$ for top $k$" metric  - `sample-rollout-membranes-x-3.csv` - postprocessed logs for a single rollout replica, `x` = each algorithm type  - `snapshots` - png snapshots of MD simulation results at different locations in the manifold
DOI: 10.5281/zenodo.11121885
title: Data and code for, "Large language models perform molecular design"

description: # Codes and data for "Large language models design sequence-defined macromolecules via evolutionary optimization"


This repository contains codes and data files for the manuscript, frozen at the time of submission. 


# Codes


## LLM codes

- `run_claude.py` - the routine for performing LLM-based rollouts; intended for command line execution using argparse

- `message_utils.py` - utilities for constructing and parsing messages for LLM I/O

- `model_utils.py` - lightweight utilities for retrieving formatted predictions from the RNN ensemble

- `target_defs.py` - defines the sequence, locations, and natural language descriptions of the target structures

- `ask_about_oracle.ipynb` - asks the LLM to speculate about the nature of the optimization task


## other algorithms

- `active_learning.ipynb` - use EI acquisition with RF surrogate to label new sequences; includes an unused tokenization scheme

- `evolutionary_algorithm.ipynb` - use DEAP library to perform evolutionary optimization

- `random_sampling.ipynb` - sample sequences randomly from all possible sequences


## postprocessing

- `process_aggregated_logs.py` - reads data from the raw log files and prepares them for visualization

- `process_sample_rollouts.py` - reads data from the raw log files and prepares individual rollouts


## visualization

- `figure1b.ipynb` - renders panel b of Fig. 1

- `figure1efg.ipynb` - renders the last row of Fig. 1 (panels e-g)

- `figure2.ipynb` - renders all of Fig. 2


# Data files


- `prompts/`

 - `prompt-scientific-v4.yml` - the full text of the scientific prompt, to be read by `run_claude.py`

 - `prompt-oracle-v4.yml` - the full text of the oracle prompt, to be read by `run_claude.py`

- `models/` - the TorchScript RNN models used to make predictions

- `data/`

 - `embeddings` - calculated embeddings for a collection of sequences from our prior work

 - `llm-logs` - the raw logs obtained from the LLM (other algorithms made to look like the LLM logs after the fact)

 - `all-rollouts-kltd.csv` - postprocessed logs for all the rollouts using the "top $k < d^*$" metric

 - `all-rollouts-topkd.csv` - postprocessed logs for all the rollouts using the "mean $d$ for top $k$" metric

 - `sample-rollout-membranes-x-3.csv` - postprocessed logs for a single rollout replica, `x` = each algorithm type

 - `snapshots` - png snapshots of MD simulation results at different locations in the manifold
DOI: 10.6084/m9.figshare.26870779
title: The genome assembly file of cultivated and wild Morinda oficinalis

description: *.fa files were the genome assembly files of config genome assembly vesion.*chr.fa files were the genome assembly files of chromosomes genome assembly vesion.Morinda_officinalis.** are cultivated species data.Ymorinda_officinalis.** are wild species data.
DOI: 10.6084/m9.figshare.26870779.v1
title: The genome assembly file of cultivated and wild Morinda oficinalis

description: *.fa files were the genome assembly files of config genome assembly vesion.*chr.fa files were the genome assembly files of chromosomes genome assembly vesion.Morinda_officinalis.** are cultivated species data.Ymorinda_officinalis.** are wild species data.
DOI: 10.15468/dl.cg2t29
title: Occurrence Download

description: A dataset containing 1304783 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Africa",
 "OccurrenceStatus is Present",
 "TaxonKey is Fabaceae"
 ]
}

 The dataset includes 1304783 records from 770 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0107773-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3886/e190701v1
title: ECIN Replication Package for "Managerial Turnover in Primary Care Clinics"

description: This is the data and code which accompanies the article "Managerial Turnover in Primary Care Clinics." The abstract of the paper is below.<br><br>We investigate the relationship between primary care clinic performance and managerial turnover. Results show that profit in a year is a strong indicator of whether the administrator will keep their job in the next year, although the clinics are certified as non-profits. The effect is asymmetric. Positive profits contribute more to an administrator’s chance of keeping their job than negative profits reduce it. In an extension analysis, we provide evidence that suggests new clinic managers improve their community’s health by increasing access to their clinics and improving the quality of healthcare provision.
DOI: 10.17909/3fmp-zj55
title: WASP-77Ab thermal emission spectrum
DOI: 10.25380/iastate.19733463
title: Global 1 km resolution daily near-surface air temperature for 2017

description: A gridded 1 km resolution global (50°S ~79°N) daily maximum and minimum near-surface air temperature dataset for 2017 that was generated using a seamless 1 km resolution land surface temperature dataset, a 30-arc second (~1 km) resolution digital elevation model (DEM) data, and air temperature observations at weather stations and a spatially varying coefficient model with sign preservation (SVCM-SP) algorithm. The gridded air temperature dataset is of great use in global studies of urban, climate, and hydrology. Documentation for this dataset can be found with the 2003 data. Data from other years is available at: https://doi.org/10.25380/iastate.c.6005185 <br> Change log: All 2017 files updated 5/12/23
DOI: 10.25380/iastate.19733463.v3
title: Global 1 km resolution daily near-surface air temperature for 2017

description: A gridded 1 km resolution global (50°S ~79°N) daily maximum and minimum near-surface air temperature dataset for 2017 that was generated using a seamless 1 km resolution land surface temperature dataset, a 30-arc second (~1 km) resolution digital elevation model (DEM) data, and air temperature observations at weather stations and a spatially varying coefficient model with sign preservation (SVCM-SP) algorithm. The gridded air temperature dataset is of great use in global studies of urban, climate, and hydrology. Documentation for this dataset can be found with the 2003 data. Data from other years is available at: https://doi.org/10.25380/iastate.c.6005185 <br> Change log: All 2017 files updated 5/12/23
DOI: 10.25380/iastate.19733463.v2
title: Global 1 km resolution daily near-surface air temperature for 2017

description: A gridded 1 km resolution global (50°S ~79°N) daily maximum and minimum near-surface air temperature dataset for 2017 that was generated using a seamless 1 km resolution land surface temperature dataset, a 30-arc second (~1 km) resolution digital elevation model (DEM) data, and air temperature observations at weather stations and a spatially varying coefficient model with sign preservation (SVCM-SP) algorithm. The gridded air temperature dataset is of great use in global studies of urban, climate, and hydrology. Documentation for this dataset can be found with the 2003 data. Data from other years is available at: https://doi.org/10.25380/iastate.c.6005185
DOI: 10.5281/zenodo.7930786
title: Extracted Data from Reviewed Studies for Platform Ecosystems Analytics SLR

description: Aggregation of data extraction results as part of a systematic literature review on platform ecosystems analytics.
DOI: 10.5281/zenodo.7930785
title: Extracted Data from Reviewed Studies for Platform Ecosystems Analytics SLR

description: Aggregation of data extraction results as part of a systematic literature review on platform ecosystems analytics.
DOI: 10.5281/zenodo.7929993
title: dendronotus_venustus_spades_01.fasta.gz

description: .
DOI: 10.5281/zenodo.7929992
title: dendronotus_venustus_spades_01.fasta.gz

description: .
DOI: 10.35078/pxu0fy
title: Replication Data for: Ficha epidemiológica de localidade: Distrito: Teófilo Otoni | Município: Coluna

description: Levantamento Triatomínico com operações de campo ocorridas em Minas Gerais pela Superintendência de Campanhas de Saúde Pública (SUCAM) e FUNASA (Fundação Nacional de Saúde), no período de 1979 a 1999, objetivando a busca da presença de vetores da doença de Chagas ou de vestígios dessa presença. A partir dela são orientadas as operações com inseticida (pt) Triatomine survey with field operations carried out in Minas Gerais by the Public Health Campaigns Superintendence (SUCAM) and FUNASA (National Health Foundation), from 1979 to 1999, aiming to search for the presence of Chagas disease vectors or traces of that presence. From it, operations with insecticide are guided (en) Encuesta de triatominos con operaciones de campo realizada en Minas Gerais por la Superintendencia de Campañas de Salud Pública (SUCAM) y FUNASA (Fundación Nacional de Salud), de 1979 a 1999, con el objetivo de buscar la presencia de vectores de la enfermedad de Chagas o rastros de esa presencia. Desde ella se orientan las operaciones con insecticida (es)
DOI: 10.25345/c5959cj24
title: MassIVE MSV000091928 - Distinct dephosphorylation site signatures of PP1 and PP2A-B55 coordinate mitotic exit.
title: Mitotic exit requires extensive dephosphorylation of Ser/Thr residues by the PP1 and PP2A-B55 protein phosphatases in human cells. Several aspects of this are poorly understood including specific substrates and determinants of phosphatase specificity. Here we develop a novel in vitro assay, MRBLE-dephos, that allows multiplexing of dephosphorylation reactions to determine phosphatase specificity. Using MRBLE-dephos, we establish amino acid preferences of the residues surrounding the phosphorylation site for PP1 and PP2A-B55, which reveals common and unique preferences for the two phosphatases. We use specific inhibition of PP1 and PP2A-B55 in mitotic exit lysates coupled with quantitative phosphoproteomics to identify more than 2000 regulated phosphorylation sites and integrate this with mitotic interactomes to obtain a comprehensive map of mitotic dephosphorylation events. Importantly, the sites dephosphorylated during mitotic exit reveal key signatures that are consistent with the MRBLE-dephos results. We use these insights to specifically alter INCENP dephosphorylation kinetics at mitotic exit resulting in defective cytokinesis underscoring the biological relevance of our determined specificity principles. Finally, we provide a comprehensive characterization of PP1 binding motifs and show how these can shape dephosphorylation and how PP1 primes its own association with these motifs at mitotic exit. Collectively we provide a framework for understanding mitotic exit regulation by dephosphorylation and novel approaches to dissect protein phosphatase specificity.