François Zielinski, Peter I. Maxwell, Timothy L. Fletcher, Stuart J. Davie, Nicodemo Di Pasquale, Salvatore Cardamone, Matthew J. L. Mills & Paul L. A. Popelier
06 September 2017
doi:10.1038/s41598-017-12600-3

The geometry optimization of a water molecule with a novel type of energy function called FFLUX is presented to bypass the traditional bonded potentials. FFLUX’s architecture is suitable to predict their IQA atomic energies for a previously unseen molecular geometry. Training of FFLUX is achieved via an in-house script called GAIA, which controls the construction of a kriging model. The GAIA protocol has five key steps: (1) sampling, (2) ab initio calculations, (3) atomic property calculations, (4) kriging model building and (5) validation. The steps are carried out sequentially, with the output of the previous step forming the input for the next step.

Debora Luana Monego, Marcelo Barcellos da Rosa, Paulo Cicero do Nascimento 
15 February 2017
 
URL:
https://www.sciencedirect.com/science/article/pii/S0308814616313139 

- Most computational studies apply to the electron transfer mechanism. A significant number of these applications have been directed towards understanding the electron transfer mechanism, and a useful tool called the FEDAM (full-electron donor-acceptor map) was developed to better evaluate this mechanism.  Hydrogen abstraction may be favored according to the radical’s nature. 

Maurizio Cossia, Vincenzo Baronea, Benedetta Mennuccib, Jacopo Tomasib

10 April 1998

What the research is about :
- new implementation of integral equation formalism version of the PCM solvation method
- this implementation number of techniques for analysis of energies and electronic properties of closed and open shell molecule at the Hartree-Fock and density functional levels
- HF calculations was implemented on closed shell systems and the present formulation is more effective then extended to DF calculations for open shell molecule

Computational method
- the solute molecule is embedded in a cavity surrounded by a polarizable medium, with the dielectric constant of the considered solvent. The cavity has molecular shape: it is formed by fused spheres, centered on solute atoms or atomic groups, according to the GEPOL algorithm
- IEF-PCM exploited in theory of integral equations
- IEF differs from the other PCM-like approaches only for G_el, in particular, in ionic solutions the ionic atmosphere affects the electrostatic solute–solvent interactions only

URL
https://www.sciencedirect.com/science/article/pii/S0009261498001067?via%3Dihub

Author: Koray Sayin, Ayhan Ungordu

Date available online: 6th Dec 2017

Method used:
1) Gauge-including-atomic-orbital (GIAO) method in vacuo. [B3LYP]
2) Density Functional Theory (DFT) used to get Molecular Electrostatic Potential (MEP) map, MEP contour and Frontier Molecular Orbitals (FMOs)
3) Molecular Docking method in water phase.

What the research is about:
The research is to investigate the structural, electronical and biological properties of theobromine and their tautomers and Ruthenium and Osmium complexes. This is to study their anti-cancer activity. This research is done to find out about other metals than Pt to be used as drug to treat cancer.

Photos: https://drive.google.com/drive/folders/13H88f3lZt-NJmTWARkraPUyWDgaU8w6u?usp=sharing 

Li-Juan Yu, Emily Golden, Nanhao Chen, Yuan Zhao, Alice Vrielink & Amir Karton (2017)

A number of experimental studies investigated the structure and catalytic mechanism of ChOx over the past two decades. The active site of ChOx is shown. With regard to the enzymatic mechanism, Sampson et al. identified three residues (Glu361, His447, and Asn485) that are significant for the enzymatic activity and Vrielink et al.^4,5 revealed that Gly120 also plays an important role in the catalytic mechanism.
The method used is the QM/MM MD simulations. Development and applications of combined QM/MM methods for enzymes have been extensively reviewed in the past. In order to obtain the barrier height of the hydride transfer, QM/MM MD simulations have been carried out for this enzyme, considering the influence from the surrounding residues to the reaction site. Then, high-level double-hybrid DFT simulations. High-level DHDFT calculations using the B2GP-PLYP functional were performed in order to obtain accurate reaction energies and barrier heights of the hydride transfer from the C3 atom of the substrate to the N5 atom of the FAD cofactor.

Takeshi Yanai, David P Tew, Nicholas C Handy
21 July 2004

-A new hybrid exchange–correlation functional named CAM-B3LYP is proposed. It combines the hybrid qualities of B3LYP and the long-range correction presented by Tawada et al. [J. Chem. Phys., in press]. We demonstrate that CAM-B3LYP yields atomization energies of similar quality to those from B3LYP, while also performing well for charge transfer excitations in a dipeptide model, which B3LYP underestimates enormously. The CAM-B3LYP functional comprises of 0.19 Hartree–Fock (HF) plus 0.81 Becke 1988 (B88) exchange interaction at short-range, and 0.65 HF plus 0.35 B88 at long-range. The intermediate region is smoothly described through the standard error function with parameter 0.33

-Coulomb-attenuating method

-URL :
https://www.sciencedirect.com/science/article/pii/S0009261404008620

Author : Arwa B. Raeis, Vladimir B. Bajic
Method :  in silico toxicologymethods
What the research about :
1)Determining the toxicity of chemicals to identify their harmful effects on humans, animals, plants, or the environment
2)In silico toxicology aims to complement existing toxicity tests to predict toxicity, prioritize chemicals, guide toxicity tests, and minimize late-stage failures in drugs design
3)The Tox-21c stresses replacing animal testing with human-relevant testing methods, either in vitro or in silico
url :  https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4785608/

MOEPGA: A novel method to detect protein complexes in yeast protein–protein interaction networks based on MultiObjective Evolutionary Programming Genetic Algorithm
Author: Buwen Caoa, Jiawei Luoa, Cheng Lianga, Shulin Wanga, Dan Song
Year: 2015
Date available online: 7 July 2015 

Method: MultiObjective Evolutionary Programming Genetic Algorithm (MOEPGA) 

 
What the research is about:

A novel MultiObjective Evolutionary Programming Genetic Algorithm (MOEPGA) which integrates multiple network topological features to detect biologically meaningful protein complexes. It is first systematically analyzes the multiobjective problem in terms of identifying protein complexes from PPI networks, and then constructs the objective function of the iterative algorithm based on three common topological properties of protein complexes from the benchmark dataset, finally describe algorithm, which mainly consists of three steps, population initialization, subgraph mutation and subgraph selection operation. To show the utility of this method, MOEPGA is compared with several state-of-the-art algorithms on two yeast PPI datasets. The experiment results demonstrate that the proposed method can not only find more protein complexes but also achieve higher accuracy in terms of fscore. Moreover, it cover a certain number of proteins in the input PPI network in terms of the normalized clustering score and  can serve as a powerful framework to detect protein complexes in yeast PPI networks, thereby facilitating the identification of the underlying biological functions
Link : https://ac.els-cdn.com/S1476927115300517/1-s2.0-S1476927115300517-main.pdf?_tid=b6b6a5d2-132c-11e8-9980-00000aacb35e&acdnat=1518794520_f41bb46d6e6de7430212894ec3d88573

DATE AVAILABLE ONLINE: 23 Oct 2015
WHAT THE RESEARCH ABOUT:
1) Three computational techniques most commonly used in HBV research are homology modeling, molecular docking, and molecular dynamics.
2) Homology modeling used to predict protein structure and to construct conformers of the viral polymerase and the HBV X protein. 
3) Molecular docking is used to predict the most likely orientation of a ligand when it is bound to a protein, as well as determining an energy score of the docked conformation. 
4) Molecular dynamics is a simulation that analyzes biomolecule motions and determines conformation and stability patterns. 
5) All of these modeling techniques have aided in the understanding of resistance mutations on HBV non-nucleos(t)ide reverse-transcriptase inhibitor binding

METHODS: homology modeling, molecular docking, and molecular dynamics.
URL: https://www.ncbi.nlm.nih.gov/pubmed/26477294 

By: Sean M McHugh, Julia R Rogers, Sarah A Solomon, Hongtao Yu, Yu-Shan Lin

1 September 2016

About: Cyclic peptides (CPs) are promising modulators of protein–protein interactions (PPIs), but their application remains challenging. It is currently difficult to predict the structures and bioavailability of CPs. The ability to design CPs using computer modeling would greatly facilitate the development of CPs as potent PPI modulators for fundamental studies and as potential therapeutics. Herein, computational methods are used to generate CP libraries for virtual screening, as well as current efforts to accurately predict the conformations adopted by CPs. These advances are making it possible to envision robust computational design of active CPs. However, unique properties of CPs pose significant challenges associated with sampling CP conformational space and accurately describing CP energetics. These major obstacles to structure prediction likely must be solved before robust design of active CPs can be reliably achieved.
Computational methods:
1)  Peplook, PEPstrMOD, PEP-FOLD, and I-TASSER ( determine conformations)

2) Molecular mechanics (to characterize the structural ensembles of CPs)

3) Macro Model (Macro Model, Schrodinger), MOE (MOE, Chemical Computing Group)

url: https://doi.org/10.1016/j.cbpa.2016.08.004

 

AUTHOR:  Ugur Mart , Changho Jung , Michihisa Koyama , Momoji Kuboa , Akira Miyamoto
DATE AVAILABLE ONLINE: 7 January 2005
METHOD: Density functional theory and molecular dynamic
WHAT THE RESEARCH IS ABOUT:
1) Investigate and compare the ionic properties of monovalent metal ions on the hydration behavior and adsorption mechanisms at the solid–aqueous solution interface.
2) Understand how water molecules behave on an oxide surface in an electrolytic solution, and how the interatomic interactions compete to arrange the molecules.
3) An MgO cluster model, which includes nine Mg and nine O atoms, was used in order to investigate the interaction of hydrated cations with oxide surface.
4) Hydration of monovalent metal ions (Li+ , Na+ , K+ and Cs+ ) was carried out by aligning five water molecules initially around the cation to analyze how water molecules interact with single cation depending on its structure-making or structure-breaking behavior.
URL: https://ac.els-cdn.com/S0169433204018082/1-s2.0-S0169433204018082-main.pdf?_tid=f96c0d74-14b5-11e8-8d64-00000aacb35f&acdnat=1518963424_5a76ae0650e8fb57d8e2a1df2c7b36a7

AUTHORS:
Golius A, Gorb L, Scott A.M, Hill F.C, Manoj Shukla, Goins A.B, Johnson D.R, Leszczynski J.
DATE AVAILABLE ONLINE:
25 January 2016
METHOD:
Quantitative Structure – Activity (Property) Relationships (QSAR/QSPR)
WHAT THE RESEARCH  IS ABOUT:
1. The affinity of various energetic compounds for a biological membrane was investigated using experimental and computational techniques. We measured octanol–water (log(K_ow)) and liposome–water (log(K_lipw)) partition coefficients for the following chemicals: trinitrotoluene (TNT), 2,4-dinitrotoluene (2,4-DNT), 2,6-dinitrotoluene (2,6-DNT), 2,4-dinitroanisole (DNAN), 2methoxy-5-nitrophenol (2M5NP), 2,4,6-trinitrobenzene (TNB), and 2,4-dinitrophenol (2,4-DNP). In order to determine log(K_lipw) experimentally, we used artificial solid supported lipid liposomes produced under trade mark TRANSIL. Log(K_ow) value were predicted with several program packages including the COSMOthermX software. Log(K_lipw) were estimated with COSMOmic as implemented in the COSMOthermX program package.
2. To characterize the ability of a substance to bioaccumulate is to consider the partition coefficient between water and a lipid pool i.e. biological membrane. In its simplest form, bioconcentration has been characterized as the ratio of the equilibrium concentrations of a chemical (solute) that partitions between n-octanol (representing the lipid fraction) and water.
3. To improve the ease and repeatability of bioconcentration measurements, recently test membranes comprised of a class of artificial membrane vesicles made up from phospholipids (liposomes) were synthesized and made commercially available.
URL:
https://www.sciencedirect.com/science/article/pii/S0045653516300108

AUTHORS :
Buu Q. Pham, Vu H. Nguyen, Thanh N. Truong
DATE AVAILABLE ONLINE :
 12 January 2016

METHOD :
Density Functional Theory
WHAT THE RESEARCH IS ABOUT :
1. The size-dependent chemistry of CO desorption from graphene ribbons was systematically studied using Density Functional Theory.
2. Two aspects of the size dependence were examined, namely the energy gap between the electronic low spin ground state and its high spin excited state and the fluctuation of the energy profiles of CO desorption reactions in the ground state.
3. To study the  effects of physical size on the relative barriers and stabilities of reaction intermediates along the CO desorption channel could be attributed to the disruption of π-conjugation of the graphene ribbon surface.
URL :
https://ezproxy.upm.edu.my:2060/science/article/pii/S0008622316300288

AUTHORS :  Satoshi Fudo, Norio Yamamoto, Michiyoshi Nukaga, Takato Odagiri, Masato Tashiro, Saburo Neya Tyuji Hoshino
DATE AVAILABLE ONLINE :
29 July 2015
METHOD :
--Molecular dynamics simulation
--ONIOM method implemented in Gaussian09
--UFF
--A general AMBER force field (GAFF)
WHAT THE RESEARCH IS ABOUT:
1. The binding mode of one of the inhibitory compounds to PA_N was investigated in detail by means of X-ray crystal structure analysis and molecular dynamics (MD) simulation.
It was observed in the crystal structure that three molecules of the same kind of inhibitor were bound to one PA_N.
2. The last binding site was not observed in previous crystallographic studies. Hence, the stability of inhibitor binding was examined by performing 100-ns MD simulation.
3. During the MD simulation, the three inhibitor molecules fluctuated at the respective binding sites at different amplitudes, while all of the molecules maintained interactions with the protein.
4.  The changes in binding mode are consistent with the results of calculation for binding free energy, in which molecule 1C had the lowest value, and with the fact that electron density was most clearly observed for molecule 1C in the crystal structure.
URL : https://www.sciencedirect.com/science/article/pii/S0968089615006306