(Q90921835)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31647645%20AND%20SRC:MED&resulttype=core&format=json

17 April 2020

title

EncoderMap(II): Visualizing Important Molecular Motions with Improved Generation of Protein Conformations (English)

1 reference

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17 April 2020

1

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17 April 2020

Andrej Berg

series ordinal

2

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17 April 2020

Christine Peter

series ordinal

4

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17 April 2020

author name string

Alok Jain

series ordinal

3

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17 April 2020

publication date

5 November 2019

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Journal of Chemical Information and Modeling

17 April 2020

published in

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17 April 2020

volume

59

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17 April 2020

issue

11

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17 April 2020

page(s)

4550-4560

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Hidden Markov models for detecting remote protein homologies

17 April 2020

cites work

1 reference

20 December 2021

https://opencitations.net/index/coci/api/v1/references/10.1021/ACS.JCIM.9B00675

Toward an accurate prediction of inter-residue distances in proteins using 2D recursive neural networks.

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20 December 2021

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End-to-End Differentiable Learning of Protein Structure

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20 December 2021

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Protein structure prediction using Rosetta

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20 December 2021

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Collective variable discovery and enhanced sampling using autoencoders: Innovations in network architecture and error function design

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20 December 2021

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Multivalent contacts of the Hsp70 Ssb contribute to its architecture on ribosomes and nascent chain interaction

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20 December 2021

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Perspective: Identification of collective variables and metastable states of protein dynamics

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20 December 2021

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Variational encoding of complex dynamics

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20 December 2021

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Designing a 20-residue protein

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20 December 2021

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Critical assessment of methods of protein structure prediction (CASP)-Round XII.

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20 December 2021

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Molecular chaperones in protein folding and proteostasis

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20 December 2021

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Energy landscape of a small peptide revealed by dihedral angle principal component analysis

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20 December 2021

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A generative, probabilistic model of local protein structure

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20 December 2021

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Improving prediction of secondary structure, local backbone angles, and solvent accessible surface area of proteins by iterative deep learning.

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20 December 2021

https://opencitations.net/index/coci/api/v1/references/10.1021/ACS.JCIM.9B00675

Identification of slow molecular order parameters for Markov model construction

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20 December 2021

https://opencitations.net/index/coci/api/v1/references/10.1021/ACS.JCIM.9B00675

Protein distance constraints predicted by neural networks and probability density functions.

1 reference

20 December 2021

https://opencitations.net/index/coci/api/v1/references/10.1021/ACS.JCIM.9B00675

Geometric diffusions as a tool for harmonic analysis and structure definition of data: diffusion maps.

1 reference

20 December 2021

https://opencitations.net/index/coci/api/v1/references/10.1021/ACS.JCIM.9B00675

GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers

1 reference

20 December 2021

https://opencitations.net/index/coci/api/v1/references/10.1021/ACS.JCIM.9B00675

Improving protein fold recognition and template-based modeling by employing probabilistic-based matching between predicted one-dimensional structural properties of query and corresponding native properties of templates

1 reference

20 December 2021

https://opencitations.net/index/coci/api/v1/references/10.1021/ACS.JCIM.9B00675

Towards a molecular basis of ubiquitin signaling: A dual-scale simulation study of ubiquitin dimers

1 reference

20 December 2021

https://opencitations.net/index/coci/api/v1/references/10.1021/ACS.JCIM.9B00675

On lines and planes of closest fit to systems of points in space

1 reference

20 December 2021

https://opencitations.net/index/coci/api/v1/references/10.1021/ACS.JCIM.9B00675

Time-lagged autoencoders: Deep learning of slow collective variables for molecular kinetics

1 reference

20 December 2021

https://opencitations.net/index/coci/api/v1/references/10.1021/ACS.JCIM.9B00675

A comprehensive assessment of sequence-based and template-based methods for protein contact prediction

1 reference

20 December 2021

https://opencitations.net/index/coci/api/v1/references/10.1021/ACS.JCIM.9B00675

Using Dimensionality Reduction to Systematically Expand Conformational Sampling of Intrinsically Disordered Peptides

1 reference

20 December 2021

https://opencitations.net/index/coci/api/v1/references/10.1021/ACS.JCIM.9B00675

The missing term in effective pair potentials

1 reference

20 December 2021

https://opencitations.net/index/coci/api/v1/references/10.1021/ACS.JCIM.9B00675

GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

1 reference

20 December 2021

https://opencitations.net/index/coci/api/v1/references/10.1021/ACS.JCIM.9B00675

De novo structure prediction of globular proteins aided by sequence variation-derived contacts

1 reference

20 December 2021

https://opencitations.net/index/coci/api/v1/references/10.1021/ACS.JCIM.9B00675

Intrinsic map dynamics exploration for uncharted effective free-energy landscapes.

1 reference

20 December 2021

https://opencitations.net/index/coci/api/v1/references/10.1021/ACS.JCIM.9B00675

From the Cover: Simplifying the representation of complex free-energy landscapes using sketch-map

1 reference

20 December 2021

https://opencitations.net/index/coci/api/v1/references/10.1021/ACS.JCIM.9B00675

Global fold determination from a small number of distance restraints

1 reference

20 December 2021

https://opencitations.net/index/coci/api/v1/references/10.1021/ACS.JCIM.9B00675

Comparative protein modelling by satisfaction of spatial restraints

1 reference

20 December 2021

https://opencitations.net/index/coci/api/v1/references/10.1021/ACS.JCIM.9B00675

Transferable neural networks for enhanced sampling of protein dynamics.

1 reference

20 December 2021

https://opencitations.net/index/coci/api/v1/references/10.1021/ACS.JCIM.9B00675

Functional specificity among Hsp70 molecular chaperones

1 reference

20 December 2021

https://opencitations.net/index/coci/api/v1/references/10.1021/ACS.JCIM.9B00675

Definition and testing of the GROMOS force-field versions 54A7 and 54B7

1 reference

20 December 2021

https://opencitations.net/index/coci/api/v1/references/10.1021/ACS.JCIM.9B00675

Using Dimensionality Reduction to Analyze Protein Trajectories

1 reference

20 December 2021

https://opencitations.net/index/coci/api/v1/references/10.1021/ACS.JCIM.9B00675

EncoderMap: Dimensionality Reduction and Generation of Molecule Conformations

1 reference

20 December 2021

https://opencitations.net/index/coci/api/v1/references/10.1021/ACS.JCIM.9B00675

Reweighted autoencoded variational Bayes for enhanced sampling (RAVE)

1 reference

20 December 2021

https://opencitations.net/index/coci/api/v1/references/10.1021/ACS.JCIM.9B00675

Identifiers

DOI

10.1021/ACS.JCIM.9B00675

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31647645%20AND%20SRC:MED&resulttype=core&format=json

17 April 2020

1 reference