(Q37974157)

26 August 2017

title

Multiscale modeling of macromolecular biosystems (English)

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26 August 2017

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5

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26 August 2017

Samuel C Flores

1

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26 August 2017

Julie Bernauer

series ordinal

2

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26 August 2017

Seokmin Shin

series ordinal

3

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26 August 2017

Ruhong Zhou

series ordinal

4

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26 August 2017

publication date

6 January 2012

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Briefings in Bioinformatics

26 August 2017

published in

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26 August 2017

volume

13

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26 August 2017

issue

4

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26 August 2017

page(s)

395-405

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Multiscale modeling of biomolecular systems: in serial and in parallel

26 August 2017

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Coarse-grained models for proteins

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Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics

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Progress and challenges in the automated construction of Markov state models for full protein systems

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Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations.

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Modeling conformational ensembles of slow functional motions in Pin1-WW

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Molecular simulation of ab initio protein folding for a millisecond folder NTL9(1-39)

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Atomistic folding simulations of the five-helix bundle protein λ(6−85).

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Taming the complexity of protein folding

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A role for both conformational selection and induced fit in ligand binding by the LAO protein

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21 January 2018

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21 January 2018

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Structural dynamics of the lac repressor-DNA complex revealed by a multiscale simulation

21 January 2018

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Overcoming entropic barrier with coupled sampling at dual resolutions

21 January 2018

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Resolution exchange simulation.

21 January 2018

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Multigraining: an algorithm for simultaneous fine-grained and coarse-grained simulation of molecular systems.

21 January 2018

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Correlating structural dynamics and function in single ribozyme molecules

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Ab initio RNA folding by discrete molecular dynamics: from structure prediction to folding mechanisms

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Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters

21 January 2018

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Knowledge-based instantiation of full atomic detail into coarse-grain RNA 3D structural models

21 January 2018

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A general module for RNA crystallization

21 January 2018

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Q: a molecular dynamics program for free energy calculations and empirical valence bond simulations in biomolecular systems.

21 January 2018

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Fast flexible modeling of RNA structure using internal coordinates.

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Folding thermodynamics of a model three-helix-bundle protein.

21 January 2018

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Simulating movement of tRNA into the ribosome during decoding

21 January 2018

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The non-Watson-Crick base pairs and their associated isostericity matrices

21 January 2018

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Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing

21 January 2018

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The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data

21 January 2018

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ModeRNA: a tool for comparative modeling of RNA 3D structure

21 January 2018

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Structural inference of native and partially folded RNA by high-throughput contact mapping

21 January 2018

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All-atom homology model of the Escherichia coli 30S ribosomal subunit.

21 January 2018

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Protein–protein docking benchmark version 4.0

21 January 2018

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Protein-protein docking tested in blind predictions: the CAPRI experiment

21 January 2018

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Docking and scoring protein interactions: CAPRI 2009

21 January 2018

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Recent Progress and Future Directions in Protein-Protein Docking

21 January 2018

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Convergence and combination of methods in protein-protein docking

21 January 2018

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MDockPP: A hierarchical approach for protein-protein docking and its application to CAPRI rounds 15-19

21 January 2018

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Performance of ZDOCK and ZRANK in CAPRI rounds 13-19.

21 January 2018

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Achieving reliability and high accuracy in automated protein docking: ClusPro, PIPER, SDU, and stability analysis in CAPRI rounds 13-19

21 January 2018

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Binding site prediction and improved scoring during flexible protein-protein docking with ATTRACT.

21 January 2018

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An integrated suite of fast docking algorithms

21 January 2018

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Strengths and weaknesses of data-driven docking in critical assessment of prediction of interactions.

21 January 2018

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A collaborative filtering approach for protein-protein docking scoring functions

21 January 2018

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Integrating atom-based and residue-based scoring functions for protein-protein docking

21 January 2018

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Community-wide assessment of protein-interface modeling suggests improvements to design methodology

21 January 2018

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Principles of flexible protein-protein docking

21 January 2018

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A generalized approach to sampling backbone conformations with RosettaDock for CAPRI rounds 13-19

21 January 2018

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SwarmDock and the use of normal modes in protein-protein docking

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIB%2FBBR077

Accounting for conformational changes during protein-protein docking

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR077

Shape complementarity of protein-protein complexes at multiple resolutions

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR077

Assessment of blind predictions of protein-protein interactions: current status of docking methods

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR077

Information-driven protein-DNA docking using HADDOCK: it is a matter of flexibility

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR077

A protein-DNA docking benchmark

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR077

A structure-based benchmark for protein-protein binding affinity

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR077

Are scoring functions in protein-protein docking ready to predict interactomes? Clues from a novel binding affinity benchmark

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR077

Simulations as analytical tools to understand protein aggregation and predict amyloid conformation

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR077

Principles governing oligomer formation in amyloidogenic peptides

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR077

Coarse-grained models for protein aggregation.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR077

Extending the PRIME model for protein aggregation to all 20 amino acids

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR077

Diversity of kinetic pathways in amyloid fibril formation

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR077

Effect of beta-sheet propensity on peptide aggregation

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR077

Amyloid aggregation on lipid bilayers and its impact on membrane permeability.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR077

Probing the mechanisms of fibril formation using lattice models

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR077

A condensation-ordering mechanism in nanoparticle-catalyzed peptide aggregation

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR077

Simulations of nucleation and elongation of amyloid fibrils

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR077

Simulating the T-Jump-Triggered Unfolding Dynamics of trpzip2 Peptide and Its Time-Resolved IR and Two-Dimensional IR Signals Using the Markov State Model Approach

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR077

Principles of stop-codon reading on the ribosome

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR077

21 January 2018

Identifiers

DOI

10.1093/BIB/BBR077

1 reference

journals/bib/FloresBSZH12

26 August 2017

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference