Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Problem-Solving

Problem-Solving

Effective problem-solving consists of two steps: 1. identifying the problem and 2. selecting the appropriate problem-solving strategy (i.e., a plan of action used to find a solution). Humans use four problem-solving strategies:

Frames: Problem Solving I

Frames: Problem Solving I

Consider a jib crane with an external load suspended from the pulley. The dimensions of the crane members are shown in the figure. A systematic analysis of the frame structure is required to determine the reaction forces at the pin joints, assuming that the pulleys are frictionless.

Frames: Problem Solving II

Frames: Problem Solving II

Consider a hydraulic hoist supporting a load of 1 kN. Assuming a simplified schematic representation of this frame structure, the force acting on BD and BF members can be determined.

Machines: Problem Solving II

Machines: Problem Solving II

Machines are complex structures consisting of movable, pin-connected multi-force members that work together to transmit forces. Consider a lifting tong carrying a 100 kg load. It comprises movable sections DAF and CBG linked together with member AB.

Theorems of Pappus and Guldinus: Problem Solving

Theorems of Pappus and Guldinus: Problem Solving

Pappus and Guldinus's theorems are powerful mathematical principles that are used for finding the surface area and volume of composite shapes. For example, consider a cylindrical storage tank with a conical top. Finding the surface area or volume can be challenging for such complex shapes. These theorems are particularly useful in calculating the volume and surface area of such systems. Here, the cylindrical storage tank with a conical top can be broken down into two simple shapes: a cylinder...

Machines: Problem Solving I

Machines: Problem Solving I

A toggle clamp is a mechanical device commonly used for holding and clamping objects in various applications, such as woodworking, metalworking, and assembly operations. Consider a toggle clamp subjected to a force of 200 N at the handle. The vertical clamping force can be calculated, provided the dimensions of the toggle clamp are known.
The toggle clamp system is a machine structure consisting of movable, pin-connected multi-force members that form a stabilized system to transmit forces. The...

You might also read

Related Articles

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

Sort by

Same author

De novo design of RNA pseudoknots with deep learning.

bioRxiv : the preprint server for biology·2026

Same author

Structures of nucleotide-bound human telomerase at several steps of its telomeric DNA repeat addition cycle.

Nature communications·2026

Same author

Template-based RNA structure prediction advanced through a blind code competition.

bioRxiv : the preprint server for biology·2026

Same author

RNA switch model for localization and translation of the myelin basic protein mRNA.

bioRxiv : the preprint server for biology·2025

Same author

Blind prediction of complex water and ion ensembles around RNA in CASP16.

bioRxiv : the preprint server for biology·2025

Same author

Compact RNA sensors for increasingly complex functions of multiple inputs.

Nature chemistry·2025

Same journal

Invaders taking over-Mollusc faunal change in volcanic barrier lakes of the Albertine Rift biodiversity hotspot.

PloS one·2026

Same journal

AI-driven molecular diversification and ligand-based optimization of macitentan derivatives targeting VEGFR1 and endothelin signaling pathways.

PloS one·2026

Same journal

Performance patterns and records in the world aquatics masters championships: Where do the most frequently represented nations among the top-ten masters swimmers come from?

PloS one·2026

Same journal

Modeling diurnal Temperature-Rainfall relationships under multicollinearity using PLS-SEM: A case study of Ghana.

PloS one·2026

Same journal

Organizational culture, social capital, and emergency capacity in primary healthcare institutions: A cross-sectional structural equation modeling study comparing ordinary and older communities.

PloS one·2026

Same journal

Impact of kidney function on the metabolome in the general population.

PloS one·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Jun 1, 2026

The Use of the Puzzle Box as a Means of Assessing the Efficacy of Environmental Enrichment

The Use of the Puzzle Box as a Means of Assessing the Efficacy of Environmental Enrichment

Published on: December 29, 2014

Four small puzzles that Rosetta doesn't solve.

¹Department of Biochemistry, Stanford University, Stanford, California, United States of America. rhiju@stanford.edu

|June 1, 2011

Summary

This summary is machine-generated.

The Rosetta software struggles with predicting structures for small proteins and RNA molecules. Current energy function limitations, not sampling issues, prevent accurate modeling of these small systems.

More Related Videos

The Innovation Arena: A Method for Comparing Innovative Problem-Solving Across Groups

The Innovation Arena: A Method for Comparing Innovative Problem-Solving Across Groups

Published on: May 13, 2022

Multimedia Battery for Assessment of Cognitive and Basic Skills in Mathematics (BM-PROMA)

Multimedia Battery for Assessment of Cognitive and Basic Skills in Mathematics (BM-PROMA)

Published on: August 28, 2021

Related Experiment Videos

Last Updated: Jun 1, 2026

The Use of the Puzzle Box as a Means of Assessing the Efficacy of Environmental Enrichment

The Use of the Puzzle Box as a Means of Assessing the Efficacy of Environmental Enrichment

Published on: December 29, 2014

The Innovation Arena: A Method for Comparing Innovative Problem-Solving Across Groups

The Innovation Arena: A Method for Comparing Innovative Problem-Solving Across Groups

Published on: May 13, 2022

Multimedia Battery for Assessment of Cognitive and Basic Skills in Mathematics (BM-PROMA)

Multimedia Battery for Assessment of Cognitive and Basic Skills in Mathematics (BM-PROMA)

Published on: August 28, 2021

Area of Science:

Computational Biology
Structural Bioinformatics
Molecular Modeling

Background:

The Rosetta software suite is widely used for macromolecule modeling and design.
Recent advancements have improved high-resolution modeling capabilities.
However, Rosetta faces challenges with predicting structures of small biomolecular systems.

Purpose of the Study:

To evaluate Rosetta's performance on small protein and RNA structure prediction problems.
To identify the limitations of Rosetta in modeling small molecular systems.
To provide model systems for improving Rosetta's energy function.

Main Methods:

Tested Rosetta on four specific small molecular systems: Trp cage, conotoxin, serine protease inhibitor loop, and UUCG RNA tetraloop.
Analyzed Rosetta's results in the context of conformational sampling and energy function accuracy.
Compared de novo models with experimentally observed conformations.

Main Results:

Rosetta demonstrated poor performance on all tested small protein and RNA puzzles.
Evidence suggests conformational sampling is adequate for these small systems.
Approximations and omissions in Rosetta's all-atom energy function limit discrimination of correct conformations.

Conclusions:

Rosetta's current all-atom energy function is insufficient for accurate atomic-resolution modeling of small macromolecules.
Foundational improvements to the energy function are needed for Rosetta to accurately model small proteins and RNA.
The tested molecular puzzles can guide future development of the Rosetta suite.