ArticlePLoS computational biology2009
Rapid sampling of molecular motions with prior information constraints.
Article in PLoS computational biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Integrating Rigidity Analysis into the Exploration of Protein Conformational Pathways Using RRT* and MC.Molecules (Basel, Switzerland) · 2021Article
- Structural Organization and Dynamics of Homodimeric Cytohesin Family Arf GTPase Exchange Factors in Solution and on Membranes.Structure (London, England : 1993) · 2019Article
- ART-RRT: As-Rigid-As-Possible search for protein conformational transition paths.Journal of computer-aided molecular design · 2019Article
- Using Spectral Representation to Classify Proteins' Conformational States.International journal of molecular sciences · 2018Article
- Structures of monomeric and oligomeric forms of theScience advances · 2018Article
- Structural Dynamics Control Allosteric Activation of Cytohesin Family Arf GTPase Exchange Factors.Structure (London, England : 1993) · 2018Article
- Maintaining and Enhancing Diversity of Sampled Protein Conformations in Robotics-Inspired Methods.Journal of computational biology : a journal of computational molecular cell biology · 2018Article
- Detecting intermediate protein conformations using algebraic topology.BMC bioinformatics · 2017Article
- As-Rigid-As-Possible molecular interpolation paths.Journal of computer-aided molecular design · 2017Article
- Structural Insight into the 14-3-3 Protein-dependent Inhibition of Protein Kinase ASK1 (Apoptosis Signal-regulating kinase 1).The Journal of biological chemistry · 2016Article
- Path Similarity Analysis: A Method for Quantifying Macromolecular Pathways.PLoS computational biology · 2015Article
- Prion Protein-Antibody Complexes Characterized by Chromatography-Coupled Small-Angle X-Ray Scattering.Biophysical journal · 2015Article
- Insights into mechanism kinematics for protein motion simulation.BMC bioinformatics · 2014Article
- MORPH-PRO: a novel algorithm and web server for protein morphing.Algorithms for molecular biology : AMB · 2013Article
- Modeling protein conformational transitions by a combination of coarse-grained normal mode analysis and robotics-inspired methods.BMC structural biology · 2013Article
- SIMS: a hybrid method for rapid conformational analysis.PloS one · 2013Article
- Structural intermediates in a model of the substrate translocation path of the bacterial glutamate transporter homologue GltPh.The journal of physical chemistry. B · 2012Article
- Detection and alignment of 3D domain swapping proteins using angle-distance image-based secondary structural matching techniques.PloS one · 2010Article
- Markov dynamic models for long-timescale protein motion.Bioinformatics (Oxford, England) · 2010Article
- Tracing conformational changes in proteins.BMC structural biology · 2010Article
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Authors and funding
4 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Proteins are active, flexible machines that perform a range of different functions. Innovative experimental approaches may now provide limited partial information about conformational changes along motion pathways of proteins. There is therefore a need for computational approaches that can efficiently incorporate prior information into motion prediction schemes. In this paper, we present PathRover, a general setup designed for the integration of prior information into the motion planning algorithm of rapidly exploring random trees (RRT). Each suggested motion pathway comprises a sequence of low-energy clash-free conformations that satisfy an arbitrary number of prior information constraints. These constraints can be derived from experimental data or from expert intuition about the motion. The incorporation of prior information is very straightforward and significantly narrows down the vast search in the typically high-dimensional conformational space, leading to dramatic reduction in running time. To allow the use of state-of-the-art energy functions and conformational sampling, we have integrated this framework into Rosetta, an accurate protocol for diverse types of structural modeling. The suggested framework can serve as an effective complementary tool for molecular dynamics, Normal Mode Analysis, and other prevalent techniques for predicting motion in proteins. We applied our framework to three different model systems. We show that a limited set of experimentally motivated constraints may effectively bias the simulations toward diverse predicates in an outright fashion, from distance constraints to enforcement of loop closure. In particular, our analysis sheds light on mechanisms of protein domain swapping and on the role of different residues in the motion.
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