Predicting loop conformational ensembles

Predicting loop conformational ensembles

<b>Motivation</b><br/> Protein function is often facilitated by the existence of multiple stable conformations. Structure prediction algorithms need to be able to model these different conformations accurately, and produce an ensemble of structures that represent a target’s conform...

Szczegółowa specyfikacja

Opis bibliograficzny
Główni autorzy:	Marks, C, Shi, J, Deane, C
Format:	Journal article
Wydane:	Oxford University Press 2017

Podobne zapisy

The conformal loop ensemble nesting field
od: Wilson, David B., i wsp.
Wydane: (2016)

Conformal loop ensembles: the Markovian characterization and the loop-soup construction
od: Werner, Wendelin, i wsp.
Wydane: (2013)

Conformal loop ensembles and the Gaussian free field
od: Watson, Samuel Stewart, 1986-
Wydane: (2015)

Increasing the accuracy of protein loop structure prediction with evolutionary constraints
od: Marks, C, i wsp.
Wydane: (2018)

Simple conformal loop ensembles on Liouville quantum gravity
od: Miller, Jason, i wsp.
Wydane: (2022)

Sphinx: Merging knowledge-based and ab initio approaches to improve protein loop prediction
od: Marks, C, i wsp.
Wydane: (2017)

Quantitative Comparison of Conformational Ensembles
od: Kevin C. Wolfe, i wsp.
Wydane: (2012-02-01)

Non-simple conformal loop ensembles on Liouville quantum gravity and the law of CLE percolation interfaces
od: Miller, Jason, i wsp.
Wydane: (2021)

Characterizing the Diversity of the CDR-H3 Loop Conformational Ensembles in Relationship to Antibody Binding Properties
od: Monica L. Fernández-Quintero, i wsp.
Wydane: (2019-01-01)

Improved protein loop prediction from sequence alone.
od: Burke, D, i wsp.
Wydane: (2001)

A novel exhaustive search algorithm for predicting the conformation of polypeptide segments in proteins.
od: Deane, C, i wsp.
Wydane: (2000)

Cellular lipids regulate the conformational ensembles of the disordered intracellular loop 3 in β2-adrenergic receptor
od: Elizaveta Mukhaleva, i wsp.
Wydane: (2024-06-01)

Antibody side chain conformations are position-dependent
od: Leem, J, i wsp.
Wydane: (2018)

Antibody H3 structure prediction
od: Marks, C, i wsp.
Wydane: (2017)

AFsample2 predicts multiple conformations and ensembles with AlphaFold2
od: Yogesh Kalakoti, i wsp.
Wydane: (2025-03-01)

Manifestly dual-conformal loop integration
od: Bourjaily, J, i wsp.
Wydane: (2019)

Molecular machine learning with conformer ensembles
od: Simon Axelrod, i wsp.
Wydane: (2023-01-01)

FREAD revisited: Accurate loop structure prediction using a database search algorithm.
od: Choi, Y, i wsp.
Wydane: (2010)

Conformational ensemble of the TNF-derived peptide solnatide in solution
od: Pau Martin-Malpartida, i wsp.
Wydane: (2022-01-01)

Transformer-Conformer Ensemble for Crash Prediction Using Connected Vehicle Trajectory Data
od: Zubayer Islam, i wsp.
Wydane: (2023-01-01)

Conformational ensemble of the human TRPV3 ion channel
od: Lejla Zubcevic, i wsp.
Wydane: (2018-11-01)

Manifestly dual-conformal loop integration
od: Jacob L. Bourjaily, i wsp.
Wydane: (2019-05-01)

Do antibody CDR loops change conformation upon binding?
od: Chu’nan Liu, i wsp.
Wydane: (2024-12-01)

Freely available conformer generation methods: how good are they?
od: Ebejer, J, i wsp.
Wydane: (2012)

Ligand-induced shifts in conformational ensembles that describe transcriptional activation
od: Sabab Hasan Khan, i wsp.
Wydane: (2022-10-01)

Applying atomistic neural networks to bias conformer ensembles towards bioactive-like conformations
od: Benoit Baillif, i wsp.
Wydane: (2023-12-01)

Loops in AdS from conformal field theory
od: Aharony, O, i wsp.
Wydane: (2017)

Conformal boundary conditions, loop gravity and the continuum
od: Wolfgang Wieland
Wydane: (2018-10-01)

Conformal correlation functions in the Brownian loop soup
od: Federico Camia, i wsp.
Wydane: (2016-01-01)

Loops in AdS from conformal field theory
od: Ofer Aharony, i wsp.
Wydane: (2017-07-01)

How long is a piece of loop?
od: Choi, Y, i wsp.
Wydane: (2013)

The H3 loop of antibodies shows unique structural characteristics
od: Regep, C, i wsp.
Wydane: (2017)

Machine Learning Generation of Dynamic Protein Conformational Ensembles
od: Li-E Zheng, i wsp.
Wydane: (2023-05-01)

Ensemble completeness in conformer sampling: the case of small macrocycles
od: Lea Seep, i wsp.
Wydane: (2021-07-01)

Conformational Ensembles Exhibit Extensive Molecular Recognition Features
od: Robert I. Cukier
Wydane: (2018-08-01)

PubChem3D: conformer ensemble accuracy
od: Kim Sunghwan, i wsp.
Wydane: (2013-01-01)

Efficient conformational ensemble generation of protein-bound peptides
od: Yumeng Yan, i wsp.
Wydane: (2017-11-01)

Comparative analysis of the CDR loops of antigen receptors
od: Wong, W, i wsp.
Wydane: (2019)

Random graph ensembles with many short loops
od: Roberts ES, i wsp.
Wydane: (2014-12-01)

Modelling conformational flexibility of kinases in inactive states
od: Schwarz, D, i wsp.
Wydane: (2019)