Evidence map›Paper›PMID 40372649›Full record

ArticleMethods in molecular biology (Clifton, N.J.)2025

Using PSICalc to Identify Protein Sequence Interdependencies.

Clark E Endsley, Matthew J Kuhl, Thomas D Townsley, Kirk K Durston, Marc Soda, T L Wallace, Joseph Deweese

Abstract read
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In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

7 authors.

Clark E EndsleyDepartment of Biological, Physical, and Human Sciences, Freed-Hardeman University, Henderson, TN, USA.
Matthew J KuhlDepartment of Biological, Physical, and Human Sciences, Freed-Hardeman University, Henderson, TN, USA.
Thomas D TownsleyIndependent Researcher, Nashville, TN, USA.
Kirk K DurstonDepartment of Research and Publications, Digital Strategies, Langley, BC, Canada.
Marc SodaIndependent Researcher, New Hanover, PA, USA.
T L WallaceDepartment of Biomedical Data Science, School of Applied Computational Sciences, Meharry Medical College, Nashville, TN, USA.
Joseph DeweeseDepartment of Biological, Physical, and Human Sciences, Freed-Hardeman University, Henderson, TN, USA. jdeweese@fhu.edu.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Protein sequence analysis has been utilized to explore features of protein structure, protein interactions, and enzyme mechanism. One approach is to compare sequences using multiple sequence alignment (MSA) and identify relationships or interdependencies within a protein sequence. This chapter will describe the Protein Sequence Interdependency Calculator (PSICalc) software tool. PSICalc is a GUI tool for analyzing protein MSAs to identify sequence interdependencies using a K modes algorithm approach. The software outputs information about sequence clusters both in graphical and in CSV format. In addition, the tool identifies sites that are invariant and nearly invariant within a group of sequences. Finally, the tool also has the ability to compare separate MSAs of two or more proteins to identify interdependencies between or among proteins.

Indexed as

Computational BiologyProteinsSequence AlignmentSequence Analysis, ProteinSoftwareAlgorithmsAmino Acid SequenceDatabases, ProteinProteinsK modesMultiple sequence alignmentProtein sequenceProtein structurePSICalcSequence interdependency

Identifiers

PMID40372649

What OpenQuestion holds

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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.