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Citations per year

Number of citations per year for the bioinformatics software tool AMBER
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Tool usage distribution map

This map represents all the scientific publications referring to AMBER per scientific context
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Protocols

AMBER specifications

Information


Unique identifier OMICS_13306
Name AMBER
Alternative name Assisted Model Building with Energy Refinement
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages C, C++, Fortran, Python
License Commercial
Computer skills Advanced
Version 17
Stability Stable
Maintained Yes

Subtools


  • AmberTools
  • MM-PBSA

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Versioning


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Documentation


Maintainers


  • person_outline D.A. Case
  • person_outline Ross Walker

Publications for Assisted Model Building with Energy Refinement

AMBER citations

 (777)
library_books

High resolution AFM structure of DNA G wires in aqueous solution

2018
Nat Commun
PMCID: 5958085
PMID: 29773796
DOI: 10.1038/s41467-018-04016-y

[…] The long G-wire models were simulated using MD approaches for relaxation in explicit solvent. The input files were prepared using xleap (AmberTools15) and simulated using Amber 10 with the ff99 DNA force field. Models underwent unrestrained energy minimization of 1000 steps of steepest decent followed by 9000 steps of conjugant gradien […]

library_books

Improvement of the activity of the anti HIV 1 integrase aptamer T30175 by introducing a modified thymidine into the loops

2018
Sci Rep
PMCID: 5945619
PMID: 29749406
DOI: 10.1038/s41598-018-25720-1

[…] ed by visual inspection and those with optimal cavity positioning and lowest energy were selected for energy minimization.Energy minimization of the docked complexes was performed using the MD engine AMBER 16. Modified thymines were renamed and their charge was calculated using antechamber. The parametrization was finally conducted with LEaP using FF14SB forcefield with explicit solvent and counte […]

library_books

Insight into resistance mechanism of anaplastic lymphoma kinase to alectinib and JH VIII 157 02 caused by G1202R solvent front mutation

2018
Drug Des Devel Ther
PMCID: 5953303
PMID: 29785088
DOI: 10.2147/DDDT.S147104

[…] a Bank (PDB), available at www.pdb.org. ALKG1202R was constructed by using EasyModeller software., Furthermore, both the crystal structure and modeled structure were refined by PyMol software and the Assisted Model Building with Energy Refinement 16 (Amber 16) simulation package, including removal of all non-bonded hetero-atoms, water molecules, addition of missing hydrogen atoms, and energy minim […]

library_books

Defining a conformational ensemble that directs activation of PPARγ

2018
Nat Commun
PMCID: 5935666
PMID: 29728618
DOI: 10.1038/s41467-018-04176-x

[…] tted to the h++ server (http://biophysics.cs.vt.edu/H++) to determine the state of titratable protons at pH 7.4, along with more realistic rotamers for some residues. This h++ PDB file was then given AMBER names for the various protonation states of histidine determined by h++ using pdb4amber (AmberTools14). PDB files of cysteine-BTFA residue was created through modification of a cysteine residue […]

library_books

Computational identification, characterization and validation of potential antigenic peptide vaccines from hrHPVs E6 proteins using immunoinformatics and computational systems biology approaches

2018
PLoS One
PMCID: 5929558
PMID: 29715318
DOI: 10.1371/journal.pone.0196484

[…] MD simulations of all the selected complexes were carried out by using AMBER 14 molecular dynamics package []. To neutralize the systems counter Na+ ions and hydrogens were added. The tleap package of Amber was utilized to perform this process. A TIP3P water box of 8.0 A […]

library_books

Substrate bound outward open structure of a Na+ coupled sialic acid symporter reveals a new Na+ site

2018
Nat Commun
PMCID: 5931594
PMID: 29717135
DOI: 10.1038/s41467-018-04045-7

[…] ch system was then solvated in a rectangular box (90 × 90 × 106 Å3) containing 150 mM Na+ and Cl− resulting in final system sizes of ~86,000 atoms. All system files were then converted from CHARMM to AMBER format with in house scripts. Simulations were carried out using the ff14SB AMBER parameter set for the protein, GLYCAM06 for the Neu5Ac, the Joung-Chetham parameters for the monovalent ions and […]


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AMBER institution(s)
Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA; Departments of Medicinal Chemistry, Pharmaceutics & Pharmaceutical Chemistry, and Bioengineering, University of Utah, Salt Lake City, UT, USA; National Institute of Environmental Health Sciences, Laboratory of Structural Biology, NC, USA; Fachbereich Biologie und Informatik, J.W. Goethe-Universität, Frankfurt/Main, Germany; Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA; Department of Chemistry, Pennsylvania State University, University Park, PA, USA; Department of Computer Science, Virgina Tech, Blacksburg, VA, USA; Department of Chemistry, Stony Brook University, Stony Brook, New York, NY, USA; Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
AMBER funding source(s)
This work was funded in part by the National Science Foundation through the Scientific Software Innovations Institutes program—NSF SI2-SSE (NSF1047875 & NSF1148276)—grants and also by the University of California (UC Lab 09-LR-06–117792) grant.

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