Calcium dependent activation of the TMEM16F scramblase and ion channel.
Paper
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The authors' code
R · 73 lines · 2.8 KB · CC-BY-4.0
- file_path <- file.choose()
- file_directory <- dirname(file_path)
- CHL <- read.csv(paste0(file_directory, "/ZFA_CLA.out"))
- A570 <- read.csv(paste0(file_directory, "/ZFA_570A.out"))
- B570 <- read.csv(paste0(file_directory, "/ZFA_570B.out"))
- A551 <- read.csv(paste0(file_directory, "/ZFA_551A.out"))
- B551 <- read.csv(paste0(file_directory, "/ZFA_551B.out"))
- # Ignore equilibration 1:716 for active. Set to 1:226 for closed state.
- POT <- POT[-(1:716), ]
- CHL <- CHL[-(1:716), ]
- A570 <- A570[-(1:716), ]
- B570 <- B570[-(1:716), ]
- A551 <- A551[-(1:716), ]
- B551 <- B551[-(1:716), ]
- # Compute boundaries, what is roughly and upper Z and lower Z plane for the pore.
- UZ <- (A570$X570A_1+B570$X570B_1)/2
- LZ <- (A551$X551A_1+B551$X551B_1)/2
- CZ <- (UZ + LZ)/2
- nUZ <- UZ - CZ # "upper" boundary (centered)
- nLZ <- LZ - CZ # "lower" boundary (centered)
- # Recenter data.
- library(dplyr)
- nCHL <- CHL %>%
- mutate(
- across(starts_with("CLA_"), ~ . - CZ) # subtract the center for each row
- )
- # Get the column names that start with “CHL_"
- cols_chl <- grep("^CLA_", names(nCHL), value = TRUE)
- # We'll store hits per column in a list
- hits_list <- vector("list", length(cols_chl))
- # A progress bar to see how the loop is going
- pb <- txtProgressBar(min = 0, max = length(cols_chl), style = 3)
- # Loop over all columns to find (-1, 0, 1) or (1, 0, -1) run-length triplets
- for (j in seq_along(cols_chl)) {
- colname <- cols_chl[j]
- # Extract numeric vector for this “CHL_j" column
- x <- nCHL[[colname]]
- # Assign -1, 0, +1 for each row i based on x[i], nLZ[i], nUZ[i]
- # Make a separate vector x_states so we don't overwrite x itself
- x_states <- numeric(length(x))
- # Below boundary -> -1
- x_states[x <= nLZ] <- -1
- # Above boundary -> +1
- x_states[x >= nUZ] <- 1
- # Inside -> 0
- inside_idx <- which(x > nLZ & x < nUZ)
- x_states[inside_idx] <- 0
- # Use RLE on x_states
- rvals <- rle(x_states)$values
- N <- length(rvals)
- # If we have < 3 runs total, we cannot form a 3-element triplet
- if (N >= 3) {
- these_hits <- logical(N - 2)
- for (i_run in seq_len(N - 2)) {
- triplet <- rvals[i_run:(i_run + 2)]
- # Check for the exact pattern
- these_hits[i_run] <- identical(triplet, c(-1, 0, 1)) ||
- identical(triplet, c(1, 0, -1))
- }
- hits_list[[j]] <- which(these_hits)
- } else {
- hits_list[[j]] <- integer(0)
- }
- setTxtProgressBar(pb, j)
- }
- close(pb)
- # Inspect results, each element of hits_list corresponds to one column.
- # hits_list[[j]] is the set of run-IDs where (-1,0,1) or (1,0,-1) was found.
- # How many hits per column
- lengths(hits_list)
- # which columns have any hits?
- which(lengths(hits_list) > 0)
AA_Closed_CLA.R, under CC-BY-4.0 · at the source
Overview
- Department of Anesthesiology, Weill Cornell Medical College, Anesthesiology,New York, NY USA
- Physiology, Biophysics and Systems Biology Graduate Program, Weill Cornell Medical College,New York, NY USA
- Department of Systems and Computational Biomedicine, Weill Cornell Medical College,New York, NY USA
- Institute for Computational Biomedicine, New York, NY USA
- Department of Biochemistry and Biophysics, Weill Cornell Medical College,New York, NY USA
Abstract
The abstract is not reproduced here: the paper's license (CC BY-NC-ND) does not allow it. Read it in the paper, at the publisher or on Europe PMC.
Repositories
Its files are read in the Code ↔ Paper reader above.
figshare 29298167
Availability: 1 check, the latest on 29 September 2026: the link answers (HTTP 200)
- 29 September 2026: the link answers (HTTP 200)
8 files
- AA_Closed_CLA.R, R, 73 lines
- AA_Closed_P.R, R, 32 lines
- AA_Closed_POT.R, R, 73 lines
- CLA_Z.sh, Shell, 20 lines
- POT_Z.sh, Shell, 20 lines
- P_Z.sh, Shell, 20 lines
- Pore_Z.sh, Shell, 32 lines
- README, Text, 21 lines
figshare 29298431
Availability: 1 check, the latest on 29 September 2026: the link answers (HTTP 200)
- 29 September 2026: the link answers (HTTP 200)
8 files
- AA_Active_CLA.R, R, 73 lines
- AA_Active_P.R, R, 32 lines
- AA_Active_POT.R, R, 73 lines
- CLA_Z.sh, Shell, 20 lines
- POT_Z.sh, Shell, 20 lines
- P_Z.sh, Shell, 20 lines
- Pore_Z.sh, Shell, 32 lines
- README, Text, 21 lines
figshare 29286710
Availability: 1 check, the latest on 29 September 2026: the link answers (HTTP 200)
- 29 September 2026: the link answers (HTTP 200)
8 files
- CG_Closed_CLA.R, R, 68 lines
- CG_Closed_PO4.R, R, 38 lines
- CG_Closed_SOD.R, R, 68 lines
- CL_Z.sh, Shell, 20 lines
- NA_Z.sh, Shell, 20 lines
- PO4_Z.sh, Shell, 20 lines
- Pore_Z.sh, Shell, 32 lines
- README, Text, 22 lines
figshare 29294237
Availability: 1 check, the latest on 29 September 2026: the link answers (HTTP 200)
- 29 September 2026: the link answers (HTTP 200)
8 files
- CG_Active_CLA.R, R, 68 lines
- CG_Active_PO4.R, R, 32 lines
- CG_Active_SOD.R, R, 68 lines
- CL_Z.sh, Shell, 20 lines
- NA_Z.sh, Shell, 20 lines
- PO4_Z.sh, Shell, 20 lines
- Pore_Z.sh, Shell, 32 lines
- README, Text, 21 lines
Code availability statement
The paper has a code availability statement. Its license (CC BY-NC-ND) does not allow reproducing it here; in short, from what the harvester recognized in it:
- it points to the authors' code: figshare 29286710, figshare 29294237, figshare 29298167, figshare 29298431
Read it in the paper: doi.org/10.1038/s41594-026-01789-5.
Tracing map
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What the map holds:
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- 28 scripts, each with its path and the digest of its content;
- no match between paragraphs and code yet;
- neither the text of the paper nor the code itself.
Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.
Data
Datasets cited
- ebi.ac.uk/
pdbe/ , at EMBL-EBI; found in “Data availability”entry - rcsb.org/
structure/ , at PDB; found in the appendix5oc9 - rcsb.org/
structure/ , at PDB; found in the appendix6qp6 - rcsb.org/
structure/ , at PDB; found in the appendix7rxg - rcsb.org/
structure/ , at PDB; found in the appendix8axj - rcsb.org/
structure/ , at PDB; found in the appendix8b8j - rcsb.org/
structure/ , at PDB; found in the appendix8b8q
Code and data availability statement
The paper has a code and data availability statement. Its license (CC BY-NC-ND) does not allow reproducing it here; in short, from what the harvester recognized in it:
- it points to a dataset: ebi.ac.uk/
pdbe/ entry - it points to the authors' code: figshare 29286710, figshare 29294237, figshare 29298167, figshare 29298431
- it says that the data are available on request
Read it in the paper: doi.org/10.1038/s41594-026-01789-5.
Versions
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Version 1, 29 September 2026: the first record
Recorded: type, language, journal, volume, issue, pages, dates, 6 authors, 3 keywords, 9 MeSH terms, 77 references, 1 RRID.
Cite
This paper
Feng, Z., Alvarenga, O. E., Di Zanni, E., Lee, S., Khelashvili, G., & Accardi, A. (2026). Calcium dependent activation of the TMEM16F scramblase and ion channel. Nature structural & molecular biology, 33(4), 664-676. https://
BibTeX
@article{feng2026calcium
author = {Feng, Zhang and Alvarenga, Omar E. and Di Zanni, Eleonora and Lee, Sangyun and Khelashvili, George and Accardi, Alessio},
title = {{Calcium dependent activation of the TMEM16F scramblase and ion channel}},
journal = {Nature structural \& molecular biology},
year = {2026},
month = apr,
volume = {33},
number = {4},
pages = {664--676},
publisher = {Nature Portfolio},
issn = {1545-9993},
doi = {10.1038/
url = {https://
pmid = {41998358},
pmcid = {PMC13095661}
}
RIS
TY - JOUR
AU - Feng, Zhang
AU - Alvarenga, Omar E.
AU - Di Zanni, Eleonora
AU - Lee, Sangyun
AU - Khelashvili, George
AU - Accardi, Alessio
TI - Calcium dependent activation of the TMEM16F scramblase and ion channel
T2 - Nature structural & molecular biology
J2 - Nat Struct Mol Biol
PY - 2026
DA - 2026/
VL - 33
IS - 4
SP - 664
EP - 676
SN - 1545-9993
PB - Nature Portfolio
DO - 10.1038/
UR - https://
LA - en
ER -
CSL-JSON
{
"id": "10.1038/
"type": "article-journal",
"title": "Calcium dependent activation of the TMEM16F scramblase and ion channel",
"container-title": "Nature structural & molecular biology",
"author": [
{
"family": "Feng",
"given": "Zhang"
},
{
"family": "Alvarenga",
"given": "Omar E."
},
{
"family": "Di Zanni",
"given": "Eleonora"
},
{
"family": "Lee",
"given": "Sangyun"
},
{
"family": "Khelashvili",
"given": "George"
},
{
"family": "Accardi",
"given": "Alessio"
}
],
"container-title-short":
"volume": "33",
"issue": "4",
"page": "664-676",
"DOI": "10.1038/
"PMID": "41998358",
"PMCID": "PMC13095661",
"ISSN": "1545-9993",
"publisher": "Nature Portfolio",
"URL": "https://
"language": "en",
"issued": {
"date-parts": [
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2026,
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17
]
]
}
}
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