Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Introduction to Test of Independence01:21

Introduction to Test of Independence

3.0K
In statistics, the term independence means that one can directly obtain the probability of any event involving both variables by multiplying their individual probabilities. Tests of independence are chi-square tests involving the use of a contingency table of observed (data) values.
The test statistic for a test of independence is similar to that of a goodness-of-fit test:
3.0K
Hypothesis Test for Test of Independence01:16

Hypothesis Test for Test of Independence

8.2K
The test of independence is a chi-square-based test used to determine whether two variables or factors are independent or dependent. This hypothesis test is used to examine the independence of the variables. One can construct two qualitative survey questions or experiments based on the variables in a contingency table. The goal is to see if the two variables are unrelated (independent) or related (dependent). The null and alternative hypotheses for this test are:
H0: The two variables (factors)...
8.2K
Law of Independent Assortment02:03

Law of Independent Assortment

62.8K
While Mendel’s Law of Segregation states that the two alleles for one gene are separated into different gametes, a different question of how different genes are inherited remains. For example, is the gene for tall plants inherited with the gene for green peas? Mendel asked this question by experimenting with a dihybrid cross; a cross in which both parents are homozygous for two distinct traits resulting in an F1 generation that are heterozygous for both traits.
62.8K
Independent and Dependent Sources01:18

Independent and Dependent Sources

2.6K
In electrical circuits, sources play a crucial role in providing power for the operation of the circuit. These sources can be broadly categorized into two types: independent and dependent.
Independent voltage or current sources supply a fixed amount of voltage or current, respectively, which is unaffected by other elements within the circuit. These are represented using specific symbols. Independent voltage sources are symbolized with polarities (+ and -), indicating the direction of the...
2.6K
Continuous Renal Replacement Therapy01:30

Continuous Renal Replacement Therapy

1.1K
Continuous Renal Replacement Therapy, also known as CRRT, is a procedural treatment for acute kidney injury (AKI) that gradually removes uremic toxins and fluids while maintaining acid-base balance and stabilizing electrolytes. It is particularly useful for hemodynamically unstable patients. Unlike intermittent hemodialysis, which is faster, CRRT provides a gentler approach over 24 hours, closely mimicking the function of natural kidneys. However, CRRT is not ideal for patients with...
1.1K
Molecular Models02:00

Molecular Models

43.8K
Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.
43.8K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

VeloRM: disentangling pre- and post-splicing RNA modification dynamics at single-cell resolution.

Nucleic acids research·2026
Same author

Artificial Intelligence Methods in Forest Biotechnology: Current Status and Future Prospects.

International journal of molecular sciences·2026
Same author

Measurement of atomic scattering factors by cryoelectron microscopy.

Proceedings of the National Academy of Sciences of the United States of America·2026
Same author

An AI-Ready Phosphorylation Meta-Analysis for <i>Saccharomyces cerevisiae</i>.

Journal of proteome research·2026
Same author

AlphaFold-driven discovery of oxysterol-binding protein-related protein-phosphoinositide 3-, 4-, and 5-phosphatase interactions using new generation confidence scores.

Protein science : a publication of the Protein Society·2026
Same author

Behavior and Speech Features of Children with ADHD.

Healthcare (Basel, Switzerland)·2026

Related Experiment Video

Updated: Feb 8, 2026

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
07:09

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

Published on: May 28, 2021

10.5K

SIMBAD: a sequence-independent molecular-replacement pipeline.

Adam J Simpkin1, Felix Simkovic1, Jens M H Thomas1

  • 1Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, England.

Acta Crystallographica. Section D, Structural Biology
|July 4, 2018
PubMed
Summary

SIMBAD is a new pipeline for molecular replacement (MR) that uses sequence-independent methods to find search models. It successfully identifies suitable models by analyzing lattice parameters and experimental data, aiding in solving challenging crystallographic structures.

Keywords:
SIMBADcontaminantlattice searchmolecular replacement pipelinestructure solution

More Related Videos

A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles
10:23

A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles

Published on: July 11, 2025

689
Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
09:34

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Published on: April 4, 2018

34.8K

Related Experiment Videos

Last Updated: Feb 8, 2026

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
07:09

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

Published on: May 28, 2021

10.5K
A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles
10:23

A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles

Published on: July 11, 2025

689
Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
09:34

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Published on: April 4, 2018

34.8K

Area of Science:

  • Crystallography
  • Structural Biology
  • Computational Biology

Background:

  • Molecular replacement (MR) traditionally relies on sequence similarity to identify search models for phasing unknown structures.
  • Sequence-based methods can fail when structural homology is low or conformational diversity is high.
  • Identifying suitable search models is crucial for solving macromolecular structures via crystallography.

Purpose of the Study:

  • To present SIMBAD, a novel sequence-independent pipeline for molecular replacement (MR).
  • To enable the identification of suitable MR search models using crystallographic data directly.
  • To address challenges in MR, including contaminant crystallization and unsequenced targets.

Main Methods:

  • SIMBAD implements a three-step pipeline for MR search model identification.
  • Step 1: Lattice-parameter search against the Protein Data Bank (PDB) for crystal form homology.
  • Step 2: Screening for crystallized contaminants using experimental data.
  • Step 3: Brute-force search using MoRDa MR software for difficult cases.

Main Results:

  • SIMBAD successfully identifies MR search models independent of sequence homology.
  • The pipeline can detect and handle cases of contaminant crystallization and mistaken identity.
  • SIMBAD has solved previously intractable crystallographic structures in early-access testing.

Conclusions:

  • SIMBAD offers a robust alternative to sequence-dependent MR search model identification.
  • The sequence-independent approach expands the applicability of MR to a wider range of targets.
  • SIMBAD facilitates the solution of challenging macromolecular structures, including unsequenced and contaminated samples.