cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.60712/si-id141887.2
title: StrainInfo SI-ID 141887.2

description: StrainInfo dataset 141887 about a strain of Agrobacterium tumefaciens. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id141888.2
title: StrainInfo SI-ID 141888.2

description: StrainInfo dataset 141888 about a strain of Agrobacterium tumefaciens. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id141889.2
title: StrainInfo SI-ID 141889.2

description: StrainInfo dataset 141889 about a strain of Agrobacterium tumefaciens. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id141890.2
title: StrainInfo SI-ID 141890.2

description: StrainInfo dataset 141890 about a strain of Agrobacterium tumefaciens. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id141891.2
title: StrainInfo SI-ID 141891.2

description: StrainInfo dataset 141891 about a strain of Agrobacterium tumefaciens. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id141892.2
title: StrainInfo SI-ID 141892.2

description: StrainInfo dataset 141892 about a strain of Agrobacterium tumefaciens. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id141893.2
title: StrainInfo SI-ID 141893.2

description: StrainInfo dataset 141893 about a strain of Agrobacterium tumefaciens. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id141894.2
title: StrainInfo SI-ID 141894.2

description: StrainInfo dataset 141894 about a strain of Agrobacterium tumefaciens. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id141895.2
title: StrainInfo SI-ID 141895.2

description: StrainInfo dataset 141895 about a strain of Agrobacterium tumefaciens. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id141896.2
title: StrainInfo SI-ID 141896.2

description: StrainInfo dataset 141896 about a strain of Agrobacterium tumefaciens. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id141897.2
title: StrainInfo SI-ID 141897.2

description: StrainInfo dataset 141897 about a strain of Agrobacterium tumefaciens. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id141898.2
title: StrainInfo SI-ID 141898.2

description: StrainInfo dataset 141898 about a strain of Agrobacterium tumefaciens. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id141899.2
title: StrainInfo SI-ID 141899.2

description: StrainInfo dataset 141899 about a strain of Agrobacterium tumefaciens. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id141900.2
title: StrainInfo SI-ID 141900.2

description: StrainInfo dataset 141900 about a strain of Agrobacterium tumefaciens. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id141901.2
title: StrainInfo SI-ID 141901.2

description: StrainInfo dataset 141901 about a strain of Agrobacterium tumefaciens. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id141902.2
title: StrainInfo SI-ID 141902.2

description: StrainInfo dataset 141902 about a strain of Agrobacterium tumefaciens. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id141903.2
title: StrainInfo SI-ID 141903.2

description: StrainInfo dataset 141903 about a strain of Agrobacterium tumefaciens. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id141904.2
title: StrainInfo SI-ID 141904.2

description: StrainInfo dataset 141904 about a strain of Agrobacterium tumefaciens. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id141905.2
title: StrainInfo SI-ID 141905.2

description: StrainInfo dataset 141905 about a strain of Agrobacterium tumefaciens. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id141906.2
title: StrainInfo SI-ID 141906.2

description: StrainInfo dataset 141906 about a strain of Agrobacterium tumefaciens. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id141907.2
title: StrainInfo SI-ID 141907.2

description: StrainInfo dataset 141907 about a strain of Agrobacterium tumefaciens. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id141908.2
title: StrainInfo SI-ID 141908.2

description: StrainInfo dataset 141908 about a strain of Agrobacterium tumefaciens. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.5281/zenodo.14961640
title: Enhancing PROTAC Ternary Complex Prediction with Ligand Information in AlphaFold 3

description: Overview

This repository contains 48 structures predicted with AlphaFold 3, and 2 molecular dynamics trajectories, reported in the publication:  



"Enhancing PROTAC Ternary Complex Prediction with Ligand Information in AlphaFold 3"  by Francisco Erazo, Nils Dunlop, Farzaneh Jalalypour, Rocío Mercado  


The accompanying code is available at: https://github.com/NilsDunlop/PROTACFold/.  

AlphaFold 3 Output Terms of Use

By using this information, you agree to the AlphaFold 3 Output Terms of Use, found at:  https://github.com/google-deepmind/alphafold3/blob/main/OUTPUT_TERMS_OF_USE.md.  

To request access to the AlphaFold 3 model parameters, follow the process outlined at:  https://github.com/google-deepmind/alphafold3.  

You may only use these parameters if received directly from Google. Use is subject to terms of use available at:  https://github.com/google-deepmind/alphafold3/blob/main/WEIGHTS_TERMS_OF_USE.md.  

All-Atom Molecular Simulations

In addition to the AlphaFold 3-predicted structures, this repository includes all-atom molecular simulations of the PROTAC ternary complex (PDB ID: 9B9W, AF3-predicted complex) using GROMACS with the Amber force field. 

Simulation Details  



Two independent 300 ns replicas (Rep1 and Rep2)  

Trajectory data saved at 5 ns intervals  


File Descriptions  

Replica 1 (Rep1) - 300 ns Simulation  



structure.gro → Structure file containing the entire system 

structure_complex.gro → Structure file containing the complex (excluding water and ions)  

Structure.tpr → Portable binary run input file  

Rep1.xtc → Trajectory file (excluding water and ions)  

Rep1.mov → QuickTime movie of the simulation  


Replica 2 (Rep2) - 300 ns Simulation



structure.gro → Structure file containing the entire system  

structure_complex.gro → Structure file containing the complex (excluding water and ions)  

Structure.tpr → Portable binary run input file  

Rep2.xtc → Trajectory file (excluding water and ions)  

Rep2.mov → QuickTime movie of the simulation  


Contact Information  

For any inquiries regarding this dataset, please contact: rocio.mercado@chalmers.se.
DOI: 10.60712/si-id141909.2
title: StrainInfo SI-ID 141909.2

description: StrainInfo dataset 141909 about a strain of Agrobacterium tumefaciens. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id141910.2
title: StrainInfo SI-ID 141910.2

description: StrainInfo dataset 141910 about a strain of Agrobacterium tumefaciens. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id141911.2
title: StrainInfo SI-ID 141911.2

description: StrainInfo dataset 141911 about a strain of Agrobacterium tumefaciens. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id141912.2
title: StrainInfo SI-ID 141912.2

description: StrainInfo dataset 141912 about a strain of Agrobacterium tumefaciens. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.15468/dl.px5yp9
title: Occurrence Download

description: A dataset containing 7591 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "PublishingCountry is Colombia",
 {
 "and" : [
 "Country is Colombia",
 {
 "not" : {
 "Issue" : [
 "is Country coordinate mismatch"
 ]
 }
 }
 ]
 }
 ]
 },
 {
 "and" : [
 "BasisOfRecord is one of (Human Observation)",
 "Country is one of (Colombia)",
 "TaxonKey is one of (Grallaria guatimalensis Prevost & Des Murs, 1842)"
 ]
 }
 ]
}

 The dataset includes 7591 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004227-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60712/si-id141913.2
title: StrainInfo SI-ID 141913.2

description: StrainInfo dataset 141913 about a strain of Agrobacterium tumefaciens. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id141914.2
title: StrainInfo SI-ID 141914.2

description: StrainInfo dataset 141914 about a strain of Agrobacterium tumefaciens. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.5281/zenodo.14959719
title: Enhancing PROTAC Ternary Complex Prediction with Ligand Information in AlphaFold 3

description: This repository contains 48 structures predicted with AlphaFold 3, reported in the publication "Enhancing PROTAC Ternary Complex Prediction with Ligand Information in AlphaFold 3" by Francisco Erazo, Nils Dunlop, Farzaneh Jalalypour, Rocío Mercado. The accompaning code is available at: https://github.com/NilsDunlop/PROTACFold/.

 

By using this information, you agree to AlphaFold 3 Output Terms of Use found at https://github.com/google-deepmind/alphafold3/blob/main/OUTPUT_TERMS_OF_USE.md.To request access to the AlphaFold 3 model parameters, follow the process set out at https://github.com/google-deepmind/alphafold3. You may only use these if received directly from Google. Use is subject to terms of use available at https://github.com/google-deepmind/alphafold3/blob/main/WEIGHTS_TERMS_OF_USE.md.
DOI: 10.60712/si-id141915.2
title: StrainInfo SI-ID 141915.2

description: StrainInfo dataset 141915 about a strain of Agrobacterium tumefaciens. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id141916.2
title: StrainInfo SI-ID 141916.2

description: StrainInfo dataset 141916 about a strain of Agrobacterium tumefaciens. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id141917.2
title: StrainInfo SI-ID 141917.2

description: StrainInfo dataset 141917 about a strain of Agrobacterium tumefaciens. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id141918.2
title: StrainInfo SI-ID 141918.2

description: StrainInfo dataset 141918 about a strain of Agrobacterium tumefaciens. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.15468/dl.q9f52s
title: Occurrence Download

description: A dataset containing 338 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Amorpha canescens Pursh",
 "Year is less than or equal to 2000",
 "Year is greater than or equal to 1970",
 {
 "or" : [
 {
 "not" : {
 "EstablishmentMeans" : [
 "is one of (MANAGED, INTRODUCED)"
 ]
 }
 },
 "EstablishmentMeans is null"
 ]
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 1000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 338 records from 41 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004188-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60712/si-id141919.2
title: StrainInfo SI-ID 141919.2

description: StrainInfo dataset 141919 about a strain of Agrobacterium tumefaciens. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id141920.2
title: StrainInfo SI-ID 141920.2

description: StrainInfo dataset 141920 about a strain of Agrobacterium tumefaciens. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id141921.2
title: StrainInfo SI-ID 141921.2

description: StrainInfo dataset 141921 about a strain of Agrobacterium tumefaciens. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id141922.2
title: StrainInfo SI-ID 141922.2

description: StrainInfo dataset 141922 about a strain of Agrobacterium tumefaciens. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id141923.2
title: StrainInfo SI-ID 141923.2

description: StrainInfo dataset 141923 about a strain of Agrobacterium tumefaciens. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id141924.2
title: StrainInfo SI-ID 141924.2

description: StrainInfo dataset 141924 about a strain of Agrobacterium tumefaciens. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id141925.2
title: StrainInfo SI-ID 141925.2

description: StrainInfo dataset 141925 about a strain of Agrobacterium tumefaciens. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id141926.2
title: StrainInfo SI-ID 141926.2

description: StrainInfo dataset 141926 about a strain of Agrobacterium tumefaciens. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id141927.2
title: StrainInfo SI-ID 141927.2

description: StrainInfo dataset 141927 about a strain of Agrobacterium tumefaciens. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id141928.2
title: StrainInfo SI-ID 141928.2

description: StrainInfo dataset 141928 about a strain of Agrobacterium tumefaciens. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id141929.2
title: StrainInfo SI-ID 141929.2

description: StrainInfo dataset 141929 about a strain of Agrobacterium tumefaciens. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id141930.2
title: StrainInfo SI-ID 141930.2

description: StrainInfo dataset 141930 about a strain of Agrobacterium tumefaciens. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id141931.2
title: StrainInfo SI-ID 141931.2

description: StrainInfo dataset 141931 about a strain of Agrobacterium tumefaciens. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id141932.2
title: StrainInfo SI-ID 141932.2

description: StrainInfo dataset 141932 about a strain of Agrobacterium tumefaciens. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id141933.2
title: StrainInfo SI-ID 141933.2

description: StrainInfo dataset 141933 about a strain of Agrobacterium tumefaciens. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id141934.2
title: StrainInfo SI-ID 141934.2

description: StrainInfo dataset 141934 about a strain of Agrobacterium tumefaciens. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id141935.2
title: StrainInfo SI-ID 141935.2

description: StrainInfo dataset 141935 about a strain of Agrobacterium tumefaciens. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id141936.2
title: StrainInfo SI-ID 141936.2

description: StrainInfo dataset 141936 about a strain of Agrobacterium tumefaciens. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id141937.2
title: StrainInfo SI-ID 141937.2

description: StrainInfo dataset 141937 about a strain of Agrobacterium tumefaciens. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id141938.2
title: StrainInfo SI-ID 141938.2

description: StrainInfo dataset 141938 about a strain of Agrobacterium tumefaciens. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id141939.2
title: StrainInfo SI-ID 141939.2

description: StrainInfo dataset 141939 about a strain of Agrobacterium tumefaciens. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id141940.2
title: StrainInfo SI-ID 141940.2

description: StrainInfo dataset 141940 about a strain of Agrobacterium tumefaciens. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id141941.2
title: StrainInfo SI-ID 141941.2

description: StrainInfo dataset 141941 about a strain of Agrobacterium tumefaciens. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id141942.2
title: StrainInfo SI-ID 141942.2

description: StrainInfo dataset 141942 about a strain of Agrobacterium tumefaciens. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id141943.2
title: StrainInfo SI-ID 141943.2

description: StrainInfo dataset 141943 about a strain of Agrobacterium tumefaciens. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id141944.2
title: StrainInfo SI-ID 141944.2

description: StrainInfo dataset 141944 about a strain of Agrobacterium tumefaciens. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id141945.2
title: StrainInfo SI-ID 141945.2

description: StrainInfo dataset 141945 about a strain of Agrobacterium tumefaciens. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id141946.2
title: StrainInfo SI-ID 141946.2

description: StrainInfo dataset 141946 about a strain of Agrobacterium tumefaciens. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.