4.7 Article

Co-evolutionary distance predictions contain flexibility information

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Biochemistry & Molecular Biology

AlphaFold2 predicts the inward-facing conformation of the multidrug transporter LmrP

Diego del Alamo et al.

Summary: In the CASP competition, AlphaFold2 generated multiple models of the LmrP protein, with one lower-ranked model potentially capturing a conformation that has not been observed in experimental structure determination so far.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2021)

Article Multidisciplinary Sciences

Improved protein structure prediction using potentials from deep learning

Andrew W. Senior et al.

NATURE (2020)

Article Biochemical Research Methods

SciPy 1.0: fundamental algorithms for scientific computing in Python

Pauli Virtanen et al.

NATURE METHODS (2020)

Article Multidisciplinary Sciences

Improved protein structure prediction using predicted interresidue orientations

Jianyi Yang et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

Article Chemistry, Medicinal

Structure- and Ligand-Based Virtual Screening on DUD-E+: Performance Dependence on Approximations to the Binding Pocket

Ann E. Cleves et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2020)

Review Biochemical Research Methods

Protein ensembles link genotype to phenotype

Ruth Nussinov et al.

PLOS COMPUTATIONAL BIOLOGY (2019)

Article Multidisciplinary Sciences

Distance-based protein folding powered by deep learning

Jinbo Xu

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)

Article Biochemistry & Molecular Biology

In silico prediction of protein flexibility with local structure approach

Tarun J. Narwani et al.

BIOCHIMIE (2019)

Review Biochemistry & Molecular Biology

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

Andriy Kryshtafovych et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2019)

Article Biochemical Research Methods

Increasing the accuracy of protein loop structure prediction with evolutionary constraints

Claire Marks et al.

BIOINFORMATICS (2019)

Article Biochemistry & Molecular Biology

Assessment of contact predictions in CASP12: Co-evolution and deep learning coming of age

Joerg Schaarschmidt et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2018)

Article Biochemistry & Molecular Biology

How is structural divergence related to evolutionary information?

Diego Zea et al.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2018)

Article Biochemistry & Molecular Biology

CABS-flex 2.0: a web server for fast simulations of flexibility of protein structures

Aleksander Kuriata et al.

NUCLEIC ACIDS RESEARCH (2018)

Article Biochemical Research Methods

DNCON2: improved protein contact prediction using two-level deep convolutional neural networks

Badri Adhikari et al.

BIOINFORMATICS (2018)

Article Biochemistry & Molecular Biology

Arpeggio: A Web Server for Calculating and Visualising Interatomic Interactions in Protein Structures

Harry C. Jubb et al.

JOURNAL OF MOLECULAR BIOLOGY (2017)

Article Biochemistry & Molecular Biology

Predicting Protein Dynamics and Allostery Using Multi-Protein Atomic Distance Constraints

Joe G. Greener et al.

STRUCTURE (2017)

Article Biochemical Research Methods

Conformational diversity analysis reveals three functional mechanisms in proteins

Alexander Miguel Monzon et al.

PLOS COMPUTATIONAL BIOLOGY (2017)

Article Biochemical Research Methods

Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model

Sheng Wang et al.

PLOS COMPUTATIONAL BIOLOGY (2017)

Article Biochemistry & Molecular Biology

PDBFlex: exploring flexibility in protein structures

Thomas Hrabe et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Biochemistry & Molecular Biology

How flexible is a protein: simple estimates using FRET microscopy

Shourjya Sanyal et al.

MOLECULAR BIOSYSTEMS (2016)

Article Multidisciplinary Sciences

Conservation of coevolving protein interfaces bridges prokaryote-eukaryote homologies in the twilight zone

Juan Rodriguez-Rivas et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)

Article Biochemistry & Molecular Biology

Improved de novo structure prediction in CASP11 by incorporating coevolution information into Rosetta

Sergey Ovchinnikov et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2016)

Article Mathematical & Computational Biology

CoDNaS 2.0: a comprehensive database of protein conformational diversity in the native state

Alexander Miguel Monzon et al.

DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION (2016)

Article Biochemical Research Methods

CCMpred-fast and precise prediction of protein residue-residue contacts from correlated mutations

Stefan Seemayer et al.

BIOINFORMATICS (2014)

Article Biochemical Research Methods

FreeContact: fast and free software for protein contact prediction from residue co-evolution

Laszlo Kajan et al.

BMC BIOINFORMATICS (2014)

Article Biochemistry & Molecular Biology

The DynaMine webserver: predicting protein dynamics from sequence

Elisa Cilia et al.

NUCLEIC ACIDS RESEARCH (2014)

Article Biochemistry & Molecular Biology

NMR methods for structural studies of large monomeric and multimeric proteins

Dominique P. Frueh et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2013)

Article Chemistry, Physical

Assessing Protein Loop Flexibility by Hierarchical Monte Carlo Sampling

Jerome Nilmeier et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2011)

Article Multidisciplinary Sciences

Protein 3D Structure Computed from Evolutionary Sequence Variation

Debora S. Marks et al.

PLOS ONE (2011)

Article Multidisciplinary Sciences

Direct-coupling analysis of residue coevolution captures native contacts across many protein families

Faruck Morcos et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)

Article Biochemical Research Methods

Biopython: freely available Python tools for computational molecular biology and bioinformatics

Peter J. A. Cock et al.

BIOINFORMATICS (2009)

Article Biochemistry & Molecular Biology

CREDO: A Protein-Ligand Interaction Database for Drug Discovery

Adrian Schreyer et al.

CHEMICAL BIOLOGY & DRUG DESIGN (2009)

Article Biochemistry & Molecular Biology

Dynameomics: Large-scale assessment of native protein flexibility

Noah C. Benson et al.

PROTEIN SCIENCE (2008)

Review Multidisciplinary Sciences

Dynamic personalities of proteins

Katherine Henzler-Wildman et al.

NATURE (2007)

Article Biochemistry & Molecular Biology

Protein flexibility and rigidity predicted from sequence

A Schlessinger et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2005)

Article Biochemistry & Molecular Biology

Protein flexibility predictions using graph theory

DJ Jacobs et al.

PROTEINS-STRUCTURE FUNCTION AND GENETICS (2001)

Article Biochemistry & Molecular Biology

The Protein Data Bank

HM Berman et al.

NUCLEIC ACIDS RESEARCH (2000)