Modeling loop backbone flexibility in receptor-ligand docking simulations (Q51334109)

3 April 2018

title

Modeling loop backbone flexibility in receptor-ligand docking simulations (English)

1 reference

3 April 2018

author

Wolfgang Wenzel

series ordinal

3

1 reference

3 April 2018

author name string

Johannes Flick

series ordinal

1

1 reference

3 April 2018

Frank Tristram

series ordinal

2

1 reference

3 April 2018

publication date

9 August 2012

1 reference

3 April 2018

Journal of Computational Chemistry

published in

1 reference

3 April 2018

volume

33

1 reference

3 April 2018

issue

31

1 reference

3 April 2018

page(s)

2504-2515

1 reference

3 April 2018

1 reference

Structure-based virtual screening of chemical libraries for drug discovery

21 January 2018

1 reference

Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database

21 January 2018

1 reference

Virtual ligand screening: strategies, perspectives and limitations

21 January 2018

1 reference

A critical assessment of docking programs and scoring functions

21 January 2018

1 reference

Fast Calculations of Electrostatic Solvation Free Energy from Reconstructed Solvent Density Using Proximal Radial Distribution Functions

21 January 2018

1 reference

Implications of protein flexibility for drug discovery

21 January 2018

1 reference

Contributions to the binding free energy of ligands to avidin and streptavidin.

21 January 2018

1 reference

Docking: successes and challenges

21 January 2018

1 reference

Structure-based virtual screening of FGFR inhibitors: cross-decoys and induced-fit effect.

21 January 2018

1 reference

Predicting absolute ligand binding free energies to a simple model site

21 January 2018

1 reference

Flexible side chain models improve enrichment rates in in silico screening

21 January 2018

1 reference

Enhanced docking with the mining minima optimizer: acceleration and side-chain flexibility

21 January 2018

1 reference

A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE).

21 January 2018

1 reference

Protein-ligand docking accounting for receptor side chain and global flexibility in normal modes: evaluation on kinase inhibitor cross docking

21 January 2018

1 reference

Efficient inclusion of receptor flexibility in grid-based protein-ligand docking

21 January 2018

1 reference

Consistent improvement of cross-docking results using binding site ensembles generated with elastic network normal modes

21 January 2018

1 reference

FLIPDock: docking flexible ligands into flexible receptors

21 January 2018

1 reference

Protein flexibility in ligand docking and virtual screening to protein kinases.

21 January 2018

1 reference

Conformer selection and induced fit in flexible backbone protein-protein docking using computational and NMR ensembles

21 January 2018

1 reference

An Evaluation of Explicit Receptor Flexibility in Molecular Docking Using Molecular Dynamics and Torsion Angle Molecular Dynamics

21 January 2018

1 reference

Modeling and selection of flexible proteins for structure-based drug design: backbone and side chain movements in p38 MAPK.

21 January 2018

1 reference

Multiple N-methylation by a designed approach enhances receptor selectivity

21 January 2018

1 reference

Ensemble docking into flexible active sites. Critical evaluation of FlexE against JNK-3 and beta-secretase.

21 January 2018

1 reference

Conformational flexibility models for the receptor in structure based drug design.

21 January 2018

1 reference

DynaDock: A new molecular dynamics-based algorithm for protein-peptide docking including receptor flexibility

21 January 2018

1 reference

ROSETTALIGAND: protein-small molecule docking with full side-chain flexibility

21 January 2018

1 reference

RosettaLigand docking with full ligand and receptor flexibility

21 January 2018

1 reference

Conformational transitions upon ligand binding: holo-structure prediction from apo conformations

21 January 2018

1 reference

Flexibility and inhibitor binding in cdc25 phosphatases

21 January 2018

1 reference

Three amino acids in the D2 dopamine receptor regulate selective ligand function and affinity.

21 January 2018

1 reference

Efficient Incorporation of Protein Flexibility and Dynamics into Molecular Docking Simulations

21 January 2018

1 reference

Induced fit, conformational selection and independent dynamic segments: an extended view of binding events

21 January 2018

1 reference

Structure and kinetics of a transient antibody binding intermediate reveal a kinetic discrimination mechanism in antigen recognition

21 January 2018

1 reference

Millisecond timescale fluctuations in dihydrofolate reductase are exquisitely sensitive to the bound ligands

21 January 2018

1 reference

Selected-fit versus induced-fit protein binding: kinetic differences and mutational analysis.

21 January 2018

1 reference

Complexity and simplicity of ligand-macromolecule interactions: the energy landscape perspective

21 January 2018

1 reference

Conformational selection or induced fit: a flux description of reaction mechanism

21 January 2018

1 reference

Relation between native ensembles and experimental structures of proteins

21 January 2018

1 reference

The role of dynamic conformational ensembles in biomolecular recognition

21 January 2018

1 reference

Intrinsic motions along an enzymatic reaction trajectory

21 January 2018

1 reference

Watching a protein as it functions with 150-ps time-resolved x-ray crystallography

21 January 2018

1 reference

Application of a Theory of Enzyme Specificity to Protein Synthesis

21 January 2018

1 reference

Ligand docking to proteins with discrete side-chain flexibility.

21 January 2018

1 reference

Ligand-induced conformational changes: improved predictions of ligand binding conformations and affinities.

21 January 2018

1 reference

Side-chain flexibility in proteins upon ligand binding

21 January 2018

1 reference

A flexible approach to induced fit docking

21 January 2018

1 reference

The ConSurf-HSSP database: the mapping of evolutionary conservation among homologs onto PDB structures.

21 January 2018

1 reference

How different are structurally flexible and rigid binding sites? Sequence and structural features discriminating proteins that do and do not undergo conformational change upon ligand binding

21 January 2018

1 reference

Electrostatics of nanosystems: application to microtubules and the ribosome

21 January 2018

1 reference

Towards accurate free energy calculations in ligand protein-binding studies

21 January 2018

1 reference

Stochastic Tunneling Approach for Global Minimization of Complex Potential Energy Landscapes

21 January 2018

1 reference

Toward better refinement of comparative models: predicting loops in inexact environments

21 January 2018

1 reference

Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling

21 January 2018

1 reference

Protein-protein docking with backbone flexibility

21 January 2018

1 reference

Prediction of Protein Loop Conformations using the AGBNP Implicit Solvent Model and Torsion Angle Sampling

21 January 2018

1 reference

Protein structure prediction and structural genomics

21 January 2018

1 reference

Managing protein flexibility in docking and its applications

21 January 2018

1 reference

PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations

21 January 2018

1 reference

The Blue Obelisk-interoperability in chemical informatics

21 January 2018

1 reference

Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation

21 January 2018

1 reference

Selectively nonselective kinase inhibition: striking the right balance

21 January 2018

1 reference

Flipped out: structure-guided design of selective pyrazolylpyrrole ERK inhibitors

21 January 2018

1 reference

Targeting the mitogen-activated protein kinase cascade to treat cancer

21 January 2018

1 reference

A pivotal role for ERK in the oncogenic behaviour of malignant melanoma?

21 January 2018

1 reference

The Ras-Raf-MEK-ERK pathway in the treatment of cancer

21 January 2018

1 reference

Balanol analogues probe specificity determinants and the conformational malleability of the cyclic 3',5'-adenosine monophosphate-dependent protein kinase catalytic subunit

21 January 2018

1 reference

Crystal Structure of the Catalytic Subunit of Cyclic Adenosine Monophosphate-Dependent Protein Kinase

21 January 2018

1 reference

What is a desirable statistical energy function for proteins and how can it be obtained?

21 January 2018

1 reference

A MAP kinase targeted by endotoxin and hyperosmolarity in mammalian cells

21 January 2018

1 reference

MKK3- and MKK6-regulated gene expression is mediated by the p38 mitogen-activated protein kinase signal transduction pathway

21 January 2018

1 reference

Identification of novel p38alpha MAP kinase inhibitors using fragment-based lead generation.

21 January 2018

1 reference

Etanercept: a review of its use in rheumatoid arthritis

21 January 2018

1 reference

Cytokines in rheumatoid arthritis: trials and tribulations

21 January 2018

1 reference

A conserved protonation-dependent switch controls drug binding in the Abl kinase

21 January 2018

1 reference

A Src-like inactive conformation in the abl tyrosine kinase domain

21 January 2018

1 reference

A general strategy for creating "inactive-conformation" abl inhibitors

21 January 2018

1 reference

Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models

21 January 2018

1 reference

Protein kinase inhibitors: insights into drug design from structure.

21 January 2018

1 reference

Assessment of programs for ligand binding affinity prediction

21 January 2018

1 reference

Semianalytical treatment of solvation for molecular mechanics and dynamics

21 January 2018

1 reference

Receptor flexibility in small-molecule docking calculations

21 January 2018

1 reference

21 January 2018

Identifiers

DOI

10.1002/JCC.23087

1 reference

3 April 2018

DBLP publication ID

journals/jcc/FlickTW12

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

3 April 2018