ROSETTALIGAND: protein-small molecule docking with full side-chain flexibility (Q51933455)

17 April 2018

title

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

1 reference

17 April 2018

author

Jens Meiler

series ordinal

1

1 reference

17 April 2018

David Baker

series ordinal

2

1 reference

17 April 2018

language of work or name

English

0 references

publication date

1 November 2006

1 reference

17 April 2018

published in

Proteins

1 reference

17 April 2018

volume

65

1 reference

17 April 2018

issue

3

1 reference

17 April 2018

page(s)

538-548

1 reference

17 April 2018

Virtual screening and fast automated docking methods.

cites work

1 reference

Crossref

https://api.crossref.org/works/10.1002%2FPROT.21086

The Protein Data Bank: a computer-based archival file for macromolecular structures

21 January 2018

1 reference

COCI

https://opencitations.net/index/coci/api/v1/citations/10.1016/S0022-2836(77)80200-3

Design of a Novel Globular Protein Fold with Atomic-Level Accuracy

5 March 2023

2 references

9 October 2024

https://opencitations.net/index/api/v1/citations/10.1126/SCIENCE.1089427

9 October 2024

https://opencitations.net/index/api/v1/references/10.1002/PROT.21086

Accurate computer-based design of a new backbone conformation in the second turn of protein L

2 references

9 October 2024

https://opencitations.net/index/api/v1/citations/10.1006/JMBI.2001.5229

9 October 2024

https://opencitations.net/index/api/v1/references/10.1002/PROT.21086

Improved side-chain modeling for protein-protein docking

2 references

9 October 2024

https://opencitations.net/index/api/v1/citations/10.1110/PS.041222905

9 October 2024

https://opencitations.net/index/api/v1/references/10.1002/PROT.21086

Native protein sequences are close to optimal for their structures

2 references

9 October 2024

https://opencitations.net/index/api/v1/citations/10.1073/PNAS.97.19.10383

9 October 2024

https://opencitations.net/index/api/v1/references/10.1002/PROT.21086

Development and current status of the CHARMM force field for nucleic acids.

1 reference

9 October 2024

https://opencitations.net/index/api/v1/references/10.1002/PROT.21086

A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance

1 reference

9 October 2024

https://opencitations.net/index/api/v1/references/10.1002/PROT.21086

Backbone-dependent rotamer library for proteins. Application to side-chain prediction

1 reference

9 October 2024

https://opencitations.net/index/api/v1/references/10.1002/PROT.21086

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

1 reference

9 October 2024

https://opencitations.net/index/api/v1/references/10.1002/PROT.21086

FDS: flexible ligand and receptor docking with a continuum solvent model and soft-core energy function

1 reference

9 October 2024

https://opencitations.net/index/api/v1/references/10.1002/PROT.21086

Computational design of protein-protein interactions

1 reference

9 October 2024

https://opencitations.net/index/api/v1/references/10.1002/PROT.21086

Empirical scoring functions. II. The testing of an empirical scoring function for the prediction of ligand-receptor binding affinities and the use of Bayesian regression to improve the quality of the model.

1 reference

9 October 2024

https://opencitations.net/index/api/v1/references/10.1002/PROT.21086

Evaluation of the FLEXX incremental construction algorithm for protein-ligand docking

1 reference

9 October 2024

https://opencitations.net/index/api/v1/references/10.1002/PROT.21086

Ligand-protein database: linking protein-ligand complex structures to binding data

1 reference

9 October 2024

https://opencitations.net/index/api/v1/references/10.1002/PROT.21086

Realistic protein-protein association rates from a simple diffusional model neglecting long-range interactions, free energy barriers, and landscape ruggedness

2 references

9 October 2024

https://opencitations.net/index/api/v1/references/10.1002/PROT.21086

9 October 2024

https://opencitations.net/index/api/v1/citations/10.1110/PS.03517304

Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: conformationally flexible docking by evolutionary programming

1 reference

9 October 2024

https://opencitations.net/index/api/v1/references/10.1002/PROT.21086

Side-chain flexibility in protein-ligand binding: the minimal rotation hypothesis

1 reference

9 October 2024

https://opencitations.net/index/api/v1/references/10.1002/PROT.21086

A review of protein-small molecule docking methods

1 reference

9 October 2024

https://opencitations.net/index/api/v1/references/10.1002/PROT.21086

Development and validation of a genetic algorithm for flexible docking

1 reference

9 October 2024

https://opencitations.net/index/api/v1/references/10.1002/PROT.21086

Modified AutoDock for accurate docking of protein kinase inhibitors

1 reference

9 October 2024

https://opencitations.net/index/api/v1/references/10.1002/PROT.21086

Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes

1 reference

9 October 2024

https://opencitations.net/index/api/v1/references/10.1002/PROT.21086

Bayesian statistical analysis of protein side‐chain rotamer preferences

1 reference

9 October 2024

https://opencitations.net/index/api/v1/references/10.1002/PROT.21086

Assessing scoring functions for protein-ligand interactions

1 reference

9 October 2024

https://opencitations.net/index/api/v1/references/10.1002/PROT.21086

An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes

2 references

9 October 2024

https://opencitations.net/index/api/v1/references/10.1002/PROT.21086

9 October 2024

https://opencitations.net/index/api/v1/citations/10.1016/S0022-2836(03)00021-4

The Protein Data Bank

1 reference

9 October 2024

https://opencitations.net/index/api/v1/references/10.1002/PROT.21086

Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations

2 references

9 October 2024

https://opencitations.net/index/api/v1/references/10.1002/PROT.21086

9 October 2024

https://opencitations.net/index/api/v1/citations/10.1016/S0022-2836(03)00670-3

Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes

1 reference

9 October 2024

https://opencitations.net/index/api/v1/references/10.1002/PROT.21086

Automated docking of flexible ligands: applications of AutoDock

1 reference

9 October 2024

https://opencitations.net/index/api/v1/references/10.1002/PROT.21086

Receptor flexibility in de novo ligand design and docking.

1 reference

9 October 2024

https://opencitations.net/index/api/v1/references/10.1002/PROT.21086

Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: a new homology modeling tool

1 reference

9 October 2024

https://opencitations.net/index/api/v1/references/10.1002/PROT.21086

Effective energy function for proteins in solution

1 reference

9 October 2024

https://opencitations.net/index/api/v1/references/10.1002/PROT.21086

High-throughput docking for lead generation

1 reference

9 October 2024

https://opencitations.net/index/api/v1/references/10.1002/PROT.21086

Protein-protein docking predictions for the CAPRI experiment

2 references

9 October 2024

https://opencitations.net/index/api/v1/references/10.1002/PROT.21086

9 October 2024

https://opencitations.net/index/api/v1/citations/10.1002/PROT.10384

Flexible protein–ligand docking by global energy optimization in internal coordinates

1 reference

9 October 2024

https://opencitations.net/index/api/v1/references/10.1002/PROT.21086

Automated docking to multiple target structures: incorporation of protein mobility and structural water heterogeneity in AutoDock

1 reference

9 October 2024

https://opencitations.net/index/api/v1/references/10.1002/PROT.21086

Knowledge-based scoring function to predict protein-ligand interactions.

1 reference

9 October 2024

https://opencitations.net/index/api/v1/references/10.1002/PROT.21086

FlexE: efficient molecular docking considering protein structure variations.

1 reference

9 October 2024

https://opencitations.net/index/api/v1/references/10.1002/PROT.21086

Computational redesign of protein-protein interaction specificity

2 references

9 October 2024

https://opencitations.net/index/api/v1/references/10.1002/PROT.21086

9 October 2024

https://opencitations.net/index/api/v1/citations/10.1038/NSMB749

Modeling structurally variable regions in homologous proteins with rosetta.

1 reference

9 October 2024

https://opencitations.net/index/api/v1/references/10.1002/PROT.21086

Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins

2 references

9 October 2024

https://opencitations.net/index/api/v1/references/10.1002/PROT.21086

9 October 2024

https://opencitations.net/index/api/v1/citations/10.1002/(SICI)1097-0134(19990101)34:1%3C82::AID-PROT7%3E3.0.CO;2-A

A fast flexible docking method using an incremental construction algorithm.

1 reference

9 October 2024

https://opencitations.net/index/api/v1/references/10.1002/PROT.21086

CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

1 reference

9 October 2024

https://opencitations.net/index/api/v1/references/10.1002/PROT.21086

DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases

1 reference

9 October 2024

https://opencitations.net/index/api/v1/references/10.1002/PROT.21086

Lead discovery using molecular docking

1 reference

9 October 2024

https://opencitations.net/index/api/v1/references/10.1002/PROT.21086

Thyrotropin-releasing hormone stimulates phosphorylation of the epidermal growth factor receptor in GH3 pituitary cells.

1 reference

9 October 2024

https://opencitations.net/index/api/v1/references/10.1002/PROT.21086

QXP: powerful, rapid computer algorithms for structure-based drug design

1 reference

9 October 2024

https://opencitations.net/index/api/v1/references/10.1002/PROT.21086

Principles of docking: An overview of search algorithms and a guide to scoring functions

1 reference

9 October 2024

https://opencitations.net/index/api/v1/references/10.1002/PROT.21086

Further development and validation of empirical scoring functions for structure-based binding affinity prediction

1 reference

9 October 2024

https://opencitations.net/index/api/v1/references/10.1002/PROT.21086

Progress in protein-protein docking: atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side-chain flexibility

2 references

9 October 2024

https://opencitations.net/index/api/v1/references/10.1002/PROT.21086

9 October 2024

https://opencitations.net/index/api/v1/citations/10.1002/PROT.20556

Identifiers

DOI

10.1002/PROT.21086

1 reference

17 April 2018

1 reference

17 April 2018