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FEP+ specifications

Information


Unique identifier OMICS_18798
Name FEP+
Alternative name Free Energy Perturbation
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Medium
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Devleena Shivakumar

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Publication for Free Energy Perturbation

FEP+ citations

 (9)
library_books

Mechanistic Insights into the Stimulant Properties of Novel Psychoactive Substances (NPS) and Their Discrimination by the Dopamine Transporter—In Silico and In Vitro Exploration of Dissociative Diarylethylamines

2018
Brain Sci
PMCID: 5924399
PMID: 29642450
DOI: 10.3390/brainsci8040063

[…] orter (rat DAT, rDAT) [] to dock each of the five compounds (). Their relative binding free energies were then calculated using alchemical free energy molecular dynamics simulations, particularly the free energy perturbation (FEP) method. The free energy predictions were subsequently compared with the experimental IC50 values that were reported earlier []. By using such in silico approaches we exp […]

library_books

Modern drug design: the implication of using artificial neuronal networks and multiple molecular dynamic simulations

2017
J Comput Aided Mol Des
PMCID: 5767208
PMID: 29134430
DOI: 10.1007/s10822-017-0085-7

[…] mbles. MD, in principle, provides a good estimation of the entropy contribution to the binding free energy of a compound and is usually carried out through a cohort of specialized techniques, such as free energy perturbation, thermodynamic integration, umbrella sampling, Jarzynski non-equilibrium pulling, multiple replica scaled regression models, explicit multiple routes sampling (from long MD) a […]

library_books

Free Energy Perturbation Calculation of Relative Binding Free Energy between Broadly Neutralizing Antibodies and the gp120 Glycoprotein of HIV 1

2017
J Mol Biol
PMCID: 5383735
PMID: 27908641
DOI: 10.1016/j.jmb.2016.11.021

[…] terface, this appears to be a daunting task, which is possibly outside of the realm of feasibility for the current state-of-the-art computational chemistry technology.All-atom, explicit solvent-based free energy perturbation (FEP) methods , , employing molecular dynamics (MD) simulation methodology, constitute the most rigorous physics-based approach to the computation of binding free energies in […]

library_books

Antibodyomics: bioinformatics technologies for understanding B‐cell immunity to HIV‐1

2017
PMCID: 5516196
PMID: 28133812
DOI: 10.1111/imr.12480

[…] ation and improved functional efficacy of antibodies directed against HIV‐1.As discussed in the prior section, MD simulations are widely used to define the conformational space of macromolecules, and free energy perturbation (FEP) methodology constitutes one of the most rigorous MD‐based approaches to determine the binding free energy for complex biological systems. FEP exploits the fact that free […]

library_books

Predicting water to cyclohexane partitioning of the SAMPL5 molecules using dielectric balancing of force fields

2016
J Comput Aided Mol Des
PMCID: 5206264
PMID: 27573982
DOI: 10.1007/s10822-016-9950-z

[…] harges, the other (submission 36) used dielectrically balanced GAFF/AM1-BCC, or G-DB, parameters. Going into the challenge, we expected the G-DB results to potentially be an improvement over the GAFF free energy perturbation calculations performed by one of the organizers. We also expected the imbalanced submission (#42) to perform more poorly than G-DB since the solute force field had not been ad […]

library_books

A theoretical investigation of DNA dynamics and desolvation kinetics for zinc finger proteinZif268

2015
BMC Genomics
PMCID: 4682422
PMID: 26677774
DOI: 10.1186/1471-2164-16-S12-S5

[…] nt loss upon complexation followed by C and A. If these base positions are dominated by T, least solvent loss is seen at the interaction interface. Our desolvation kinetics data obtained from running free energy perturbation also corroborates the assumption in theory that greater the loss of bulk solvent at the interaction interface of ZFP-DNA complexation stronger the binding affinity and stabili […]

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FEP+ institution(s)
Schrodinger, Inc., New York, NY, USA; Schrodinger, Inc., Portland, OR, USA

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