DRUG DESIGN PROJECT

1. Quantum Computation Part

1. 3D structure of Fluorouracil drug in the WebMo server and
performance of Geometry optimization, frequency, and molecular
orbital calculations in the gas phase

Fig: Geometry optimization

Fig: Vibrational Frequencies

2. Optimization & Frequency Calculation

3. A table for HOMO, HOMO-1, HOMO-2, LUMO, LUMO+1, and

LUMO+2, HOMO-LUMO gap of the Fluorouracil drug
Orbital Eigen value

HOMO -0.371au

HOMO-1 -0.441au

HOMO-2 -0.458au

LUMO 0.093au

LUMO+1 0.163au

LUMO+2 0.180au

HOMO-LUMO -0.464au
4. A table for the electronic energy (E), enthalpy (H), Gibbs free
energy (G), and dipole moment (Debye) of Fluorouracil drug
Electronic Energy Enthalpy (H) Gibbs Free Dipole
(E) Energy (G) Moment (Debye)
-504.442434 -504.441490 -504.480347 2.6986 Debye
Hartree Hartree Hartree

5. Image for the HOMO and LUMO orbital of the Fluorouracil drug

Fig: Homo Fig: Lumo

 2. Molecular Modeling
1. Three-dimensional protein structure used the sequence through
the AlphaFold and Swiss model online web tools
 By comparing the structures it can be said that there are a few
differences in the 3D structures. There are the pictures from Discovery
Studio

Fig: AlphaFold2

Fig: Swiss model

2. Assessment of the AlphaFold rank 1 3D structure using the
Procheck validation server & the active site of the predicted 3D
structure using the Castp server

Fig: Procheck Validation Fig: Ramachandran Plot

Fig: Errat Fig: Verify 3D

Fig: Active site prediction

Fig: Sequence
 3. Molecular Docking Part

1. The Catechin gallate(PubChem CID-5276454), and

Omeprazole(PubChem CID-4594) drugs were downloaded in sdf
format from the PubChem database
2. The protein [PDB id: 4A5S] was prepared in Pymol/Discovery
studio and optimized it with SwissPDB viewer
3. Molecular docking between the drugs and the receptor protein
was performed by PyRX (Autodock Vina) and report of the grid box
size and the binding energies (in a table)
Grid box size:
Table of the Binding Energies:

Ligand Binding Affinity rmsd/ub rmsd/lb

4a5s_Clean_M_5276454_mmff94_E=55.42 -9.1 0 0

4a5s_Clean_M_5276454_mmff94_E=55.42 -8.7 7.31 1.842

4a5s_Clean_M_5276454_mmff94_E=55.42 -8.4 5.586 3.378

4a5s_Clean_M_5276454_mmff94_E=55.42 -8.1 27.81 22.536

4a5s_Clean_M_5276454_mmff94_E=55.42 -7.9 33.993 31.597

4a5s_Clean_M_5276454_mmff94_E=55.42 -7.9 26.298 23.576

4a5s_Clean_M_5276454_mmff94_E=55.42 -7.8 34.432 31.827

4a5s_Clean_M_5276454_mmff94_E=55.42 -7.8 4.855 2.437

4a5s_Clean_M_5276454_mmff94_E=55.42 -7.7 7.969 3.23

4a5s_Clean_M_4594_mmff94_E=56.34 -7.6 0 0

4a5s_Clean_M_4594_mmff94_E=56.34 -7.1 33.285 30.832

4a5s_Clean_M_4594_mmff94_E=56.34 -7.1 32.668 30.611

4a5s_Clean_M_4594_mmff94_E=56.34 -7 34.874 33.872

4a5s_Clean_M_4594_mmff94_E=56.34 -7 2.273 1.467

4a5s_Clean_M_4594_mmff94_E=56.34 -6.9 35.125 33.948

4a5s_Clean_M_4594_mmff94_E=56.34 -6.9 33.887 31.52

4a5s_Clean_M_4594_mmff94_E=56.34 -6.9 34.265 31.866

4a5s_Clean_M_4594_mmff94_E=56.34 -6.8 30.447 28.453

4. Collection of 5 non-bonding interactions (in a table) of drugs with
amino acids and taking a picture by Discovery studio
N:UNK1:H -
A:ARG125:HH2 N:UNK1:H - N:UNK1:H - A:GLU205:OE N:UNK1:H -
Name 1 - N:UNK1:O A:GLU205:O A:GLU205:O2 2 A:TYR662:OH

Visible Yes Yes Yes Yes Yes

Color

Ligand Non-bond Ligand Non- Ligand Non- Ligand Non- Ligand Non-
Parent Monitor bond Monitor bond Monitor bond Monitor bond Monitor

Distance 2.64948 2.19913 2.83386 2.4255 2.08439

Category Hydrogen Bond Hydrogen Bond Hydrogen Bond Hydrogen Bond Hydrogen Bond

Conventional Conventional Conventional Conventional Conventional

Types Hydrogen Bond Hydrogen Bond Hydrogen Bond Hydrogen Bond Hydrogen Bond

From A:ARG125:HH21 N:UNK1:H N:UNK1:H N:UNK1:H N:UNK1:H

From
Chemistr
y H-Donor H-Donor H-Donor H-Donor H-Donor

To N:UNK1:O A:GLU205:O A:GLU205:O A:GLU205:OE2 A:TYR662:OH

To
Chemistr
y H-Acceptor H-Acceptor H-Acceptor H-Acceptor H-Acceptor

Angle 109.248 127.623 150.415 109.447 174.793

DHA
Angle
HAY 124.931 150.676 138.202 91.131 98.304

Fig: 3D diagram of Receptor-ligand interactions

 Fig: 2D diagram of Receptor-ligand interactions
4. Pharmacophore Modeling
1. Enhancing the Medicinal quality of Tubocurarine chloride by
eliminating problematic substructures while adhering to Lipinsky,
Pfizer, GSK and Golden rule [ADMETlab 3.0]
Medicinal qualities of Tubocurarine chloride:
 We obtain [1-(4-((3-(ethyl(oxo)ammonio)pentyl)oxy)benzyl)-6,7-
dihydroxy-1,2,3,4-tetrahydroisoquinoline] after the modification of
Tubocurarine chloride
 Modified Canonical Smiles is: CCC([N+]
(CC[H])=O)CCOC(C=C1)=CC=C1CC2C3=CC(O)=C(O[H])C=C3CCN2

Table: Comparison of Medicinal chemistry of Tubocurarine chloride

and [1-(4-((3-(ethyl(oxo)ammonio)pentyl)oxy)benzyl)-6,7-
dihydroxy-1,2,3,4-tetrahydroisoquinoline]
 1-(4-((3-
Medicinal (ethyl(oxo)ammonio)pentyl)oxy)benzyl)-
Tubocurarine Chloride
chemistry 6,7-dihydroxy-1,2,3,4-
tetrahydroisoquinoline

QED 0.245(Unattractive) 0.44(Unattractive)

SAscore Easy Easy

GASA Hard Easy

Fsp3
0.351 0.478

MCE-18 136.12 57.176

NPscore 2.261 0.64

Lipinski Rule Accepted Accepted

Pfizer Rule Accepted Accepted

GSK Rule Rejected Accepted

Golden Triangle Rejected Accepted

PAINS 0 1

Alarm_NMR Rule 1 2

BMS Rule 0 0

Chelating Rule 1 1
Colloidal
aggregators 1 0.912

FLuc inhibitors 0.003 0.008

Blue fluorescence 0.6 0.146

Green fluorescence 0.662 0.667

 Reactive
compounds 0.003 0.006
Promiscuous
compounds 0.171 0.079

2. Table: Comparison of ADME properties of Tubocurarine chloride

and [1-(4-((3-(ethyl(oxo)ammonio)pentyl)oxy)benzyl)-6,7-
dihydroxy-1,2,3,4-tetrahydroisoquinoline]
1-(4-((3-
Tubocurarine (ethyl(oxo)ammonio)pentyl)oxy)benzyl)-6,7-
Properties Parameter chloride dihydroxy-1,2,3,4-tetrahydroisoquinoline

Caco-2
Permeability -5.453 -5.492
MDCK
Permeability 0 0
PAMPA --- --
Pgp
inhibitor --- ---
Pgp
ABSPORPTION substrate +++ --
HIA - ---
F20% +++ ++
F30% +++ -
F50% +++ +++
PPB 46.30% 45.90%
VDss 0.408 0.725
BBB --- ---
Fu 56.30% 50.60%
OATP1B1
inhibitor - +++
OATP1B3
inhibitor + +++
BCRP
DISTRIBUTION inhibitor - ---
MRP1
inhibitor +++ +++
BSEP
inhibitor ++ +++
CYP1A2
inhibitor --- ---
CYP1A2 +++ +++
substrate
 CYP2C19
inhibitor --- ---
CYP2C19
substrate +++ +++
CYP2C9
inhibitor --- ---
CYP2C9
substrate - ++
CYP2D6
inhibitor --- +++
CYP2D6
substrate +++ +++
CYP3A4
inhibitor --- ---
CYP3A4
substrate --- ---
CYP2B6
inhibitor -- -
CYP2B6
substrate +++ ---
CYP2C8
inhibitor --- ---
HLM
Stability --- +++
EXCRETION CLplasma 3.419 16.196
T1/2 2.992 1.729
Table: Comparison of Toxicity properties of Tubocurarine chloride
and [1-(4-((3-(ethyl(oxo)ammonio)pentyl)oxy)benzyl)-6,7-
dihydroxy-1,2,3,4-tetrahydroisoquinoline]
1-(4-((3-
(ethyl(oxo)ammonio)pentyl)oxy)benzyl
)-6,7-dihydroxy-1,2,3,4-
TOXICITY Tubocurarine chloride tetrahydroisoquinoline
hERG Blockers 0.726 0.636
hERG Blockers
(10um) 0.752 0.875
DILI 0 0.26
AMES Toxicity 0.073 0.799
Rat Oral Acute
Toxicity 0.943 0.585
FDAMDD 0.999 0.676
Skin Sensitization 0.851 0.972
Carcinogenicity 0.577 0.379
Eye Corrosion 0 0
Eye Irritation 0.038 0.629
Respiratory 1 0.887
Human
Hepatotoxicity 0.013 0.321
Drug-induced
Nephrotoxicity 0.007 0.147
Drug-induced
Neurotoxicity 0.537 0.082
Ototoxicity 0.262 0.65
Hematotoxicity 0.001 0.108
Genotoxicity 0.457 1
RPMI-8226
Immunitoxicity 0.034 0.06
A549 Cytotoxicity 0 0.158
Hek293 Cytotoxicity 0.76 0.786
BCF 1.889 1.529
IGC50 4.724 4.208
LC50DM 6.285 5.424
LC50FM 5.581 4.955
 According to Lipinski’s rule of five, a compound with no more than five
hydrogen bond donors and 10 hydrogen bond acceptors is a good
pharmacophore and partition coefficient log P should not exceed 5.
 The Ghose filter selects a compound as a good pharmacophore which
has log P in -0.4 to 5.6 and the molecular weight in 180 to 480.
 Veber’s rule states that a good pharmacophore should have 10 or
fewer rotatable bonds, and the polar surface should not exceed 140.
 SO,according to these rules [1-(4-((3-
(ethyl(oxo)ammonio)pentyl)oxy)benzyl)-6,7-dihydroxy-1,2,3,4-
tetrahydroisoquinoline] is better in terms of pharmacokinetics than
Tubocurarine chloride

3. ZINC ID of five compounds with similar pharmacophore as

Morphine
 Open the server Zincpharmer
 Click search zinc
  Click load features & then upload the sdf file of 3D conformer
of Morphine

 Click to submit query after cancelling selections of some

pharmacophores
Five ZINC id:

5. Molecular Dynamics Simulation

1. Material and Methods and ‘Result’ section of the graph
Materials and Methods:
 1. Filtering Unwanted Sub-Substructures with Physiochemical
Analysis
In virtual screening, undesirable chemical components or molecular
structures are eliminated based on their chemical properties in order
to prevent side effects and false positive results in drug discovery. This
technique is known as filtering unwanted sub-substructures with
physiochemical analysis. Initially, a thorough literature review was
used to list medicinal plants and the phytochemicals that
corresponded to them that were discovered by GC-MS and showed
anti-diabetic characteristics (Supplementary Table S1). substances for
Brenk properties, NIH properties, and pan-assay interference
substances (PAINS) were evaluated using RDKit version
2023.03.Phenol-sulfonamides, rhodanines, phenol-esters, curcumin,
enones, hydroxyphenyl hydrazones, catechols, toxoflavin,
isothiazolones, analine, and quinones were among the often
encountered undesired substructures. Using RDKit v2023.03, several
descriptors such as molecular weight, rotatable bonds, hydrogen
acceptor and donor, MLogP, TPSA, hetero atoms, molar refractivity,
and aromatic rings were calculated in order to determine the various
physicochemical and molecular properties of phytochemicals.
Molecular weight: 200–480, mlogp: −0.4–4.15, hetero atoms: >1, MR:
≥40–130, and TPSA: ≤131.6 were the physiological parameters that
were set. In the initial phases of computational drug development,
 these standards are frequently applied as filters to weed out
compounds.

 2. Virtual Screening via Molecular Docking

Molecular docking uses computational methods to anticipate the
binding interactions between ligands and target proteins, which aids in
the identification of possible therapeutic candidates and the
comprehension of their binding mechanisms. We downloaded all of
the filtered substances in 3D SDF format from the PubChem database.
The steepest descent optimization algorithm steps 2000 was employed
using PyRx software v0.8, and all ligand optimizations and energy
reduction utilizing the mmff94 force field were used. The three-
dimensional X-ray crystal structure of the DPP-4 receptor (PDB ID:
4a5s) was obtained in pdb format from the RCSB Protein Data Bank. To
create the protein structure, hydrogen was added after all
heteroatoms and water molecules were eliminated. Then, using the
ff19SB force field with the YASARA software, version 21.12.19, the
cleaned protein structure was optimized and energy was reduced. A
molecular docking investigation was conducted using the molecular
docking tool AutoDock Vina v4.2.6. PDB was converted into PDBQT
format for the docking analysis's protein and ligand input using
AutoDock Vina.Docking was conducted in a 30 × 30 × 30 grid box with
the following center values: x = 26.85, y = 12.60, z = 58.94;
corresponding dimensions were recorded: x = 51.35, y = 66.93, and z =
59.60 Å. Stronger binding affinities were indicated by negative values,
which were used to compute and order the docking results. The
reference N7F inhibitor, which was bound with 4a5s, was also docked
to the target protein in order to confirm the results of the docking
investigation. Using Discovery Studio Visualizer, all docking postures
and 2D and 3D protein-ligand interactions were seen and examined.

 3. ADME/Tox and Bioactivity Analysis

Early toxicological evaluation of a molecule is essential in the realm of
medication discovery and design. To ascertain a compound's toxicity,
an in vivo animal model has traditionally been employed. But this
method is expensive, time-consuming, and fraught with moral
dilemmas. As a result, the silico toxicity assay of chemical compounds
 using computer-aided medication design can be regarded as helpful.
Using the standard simplified molecular-input line-entry system
(SMILES) specification as the input syntax, the ProTox-II server was
employed to forecast the toxicity of the selected compounds. Two
freely accessible online servers, SwissADME and pKCSM, were utilized
to calculate the compound's absorption, distribution, metabolism, and
excretion (ADME) characteristics. The chosen compound's varied
pharmacokinetic and pharmacodynamic properties were ascertained
and predicted with the assistance of both servers. The Molinspiration
server was used to assess the biological activity of three different
chemicals. Bioactive chemicals were identified by a bioactivity score of
>0 in this case, −5.0 to <0 for moderately active compounds, and <−5.0
for physiologically inert compounds.

 4. Density Functional Theory (DFT) Calculation

Because DFT is based on quantum mechanics, it can calculate a variety
of parameters, including molecular energies, geometries, and
electronic properties. It also provides an extremely accurate
representation of the distribution of electrons within a molecule. The
different quantum mechanical properties were calculated using the
Gaussian 09 W software program. Using density functional theory
using a basis set of 6–311 g(d,p) correlation functions, the electronic
characteristics of the molecules were calculated in their singlet ground
state, free of charge and solvent, using the B3LYP (Becke, 3-parameter,
Lee-Yang-Parr) approach. Several reactivity descriptors, including
electron affinity, ionization potential, electronegativity (χ), electronic
potential (μ), chemical hardness (η), chemical softness (ζ), and
electrophilicity (ω), were investigated using the DFT method in order
to evaluate the molecule's reactivity.

 5. Molecular Dynamics Simulation

A computational method known as molecular dynamics (MD)
simulation mimics the temporal motion and behavior of atoms and
molecules, enabling the study and modeling of their dynamic
interactions in various systems. On the chosen docked complexes,
molecular dynamics simulations were run in order to comprehend the
structural alterations along the simulation paths.The YASARA dynamics
 software (version 21.12.19) was utilized to conduct the simulations,
with all computations utilizing the AMBER14ffSB force field. While
short-range van der Waals and Coulomb interactions were examined
within an 8 Å cutoff radius, long-range electrostatic interactions were
calculated using the particle mesh Ewald method. Temperature and
pressure were monitored during the simulations using a Monte Carlo
barostat and a Langevin thermostat, respectively. The entire setup
included a water solvent system, pH 7.4, 0.9% NaCl concentration, and
a temperature of 298 K. Using the steepest descent algorithm, the
system was minimized. To examine the trajectory data, snapshots
were obtained at 100 ps intervals during the simulations, which used a
time step of 1.25 fs for a total period of 100 ns [77]. The number of
hydrogen bonds, SASA, RG, RMSD, and RMSF were among the
characteristics that were examined using the simulated trajectories.
The charts produced by the MD simulations were displayed using the
Matplotlib Python library.

 6. MM-PBSA Estimation and Free Energy Landscape Analysis

Using the MM-PBSA approach, the binding free energies of the
compounds generated between proteins and ligands were measured
using the results of MD simulations. In situations such as protein–
ligand binding interactions, this is a dependable and efficient method
for modeling molecular recognition and simulating free energy [84].
The YASARA Dynamics framework's md_analyzebindenergy.mcr was
utilized to compute ligand binding energies. This method's
fundamental principle is to dissect the complex's total free energy into
its constituent parts, which include elements like electrostatic, van der
Waals, and solvation energies.The binding free energy was estimated
using the following equation:
ΔGbind = ΔGcomplex − [ΔGprotein + ΔGligand]
This equation can be further detailed as ΔGbind = ΔGMM + ΔGPB +
ΔGSA-TΔS.
The molecular mechanics interaction (ΔGMM) in this case is the
product of the electrostatic and van der Waals interactions; the polar
and non-polar solvation energies are denoted by ΔGPB and ΔGSA,
respectively, and the entropic contribution is represented by TΔS.
 When a molecule transitions between different conformations or
states, it explores both favorable states and energy hurdles, which are
represented by a free energy landscape (FEL). The simulation
trajectories were used to calculate the RMSD and RG values for each
frame. This resulted in the formation of a density matrix that defined a
specific region of the conformational space. Using the density matrix
and statistical mechanics, the Gibbs free energy surface was then
calculated. With Matplotlib v3.7.2, the 2D and 3D plot visualizations
were produced.

 Results and Discussion

DPP-4 inhibition has been linked to increases in beta cell mass and
functionality in a number of diabetic models, as well as a decrease in
diabetes-induced beta cell dysfunction in in vitro and pre-clinical
investigations. Medicines made from plants have been used for
thousands of years. Medicinal plant inhibitors have been utilized as
supplemental therapies to treat a variety of illnesses, including
diabetes mellitus and cardiovascular disorders. To find new treatments
for diabetes mellitus, we have conducted a number of trials and built a
library of phytochemicals.

6. Vaccine design
1. BCL epitopes, CTL epitopes and HTL from Matrix protein
(Gene: M) of Nipah Virus in a Table with appropriate allergenicity,
antigenicity and toxicity
Table: BCL Epitopes (ABCPred)
Ran Position Epitope VaxiJen AllerTop ToxinPred
k
1 46 KYKIYTPGANERKYNN ANTIGEN NON- Non-Toxin
ALLERGEN
3 21 PSSWEHGGYLDKVEPE ANTIGEN NON- Non-Toxin
ALLERGEN
6 86 IRTIAAYPLGVGKSAS ANTIGEN NON- Non-Toxin
ALLERGEN

Table: MHC-II Epitope (NetMHCIIpan 4.1)

Ran Position Epitope VaxiJen AllerTop ToxinPred
k
45 PKYKIYTPGANERKY ANTIGEN NON- Non-Toxin
ALLERGEN
80 TGKRKKIRTIAAYPL ANTIGEN NON- Non-Toxin
ALLERGEN
81 GKRKKIRTIAAYPLG ANTIGEN NON- Non-Toxin
ALLERGEN

Table: MHC-I Epitope (NetMHCpan 4.1)

Rank Position Epitope VaxiJen AllerTop ToxinPred
296 KNLCFSLMDINPWL ANTIGEN NON- Non-Toxin
ALLERGEN
163 IQLDKHQALRIFFL ANTIGEN NON- Non-Toxin
ALLERGEN
224 SLDKDGFKVASFML ANTIGEN NON- Non-Toxin
ALLERGEN

2. Constructing the Vaccine and their physiochemical properties,

secondary structure, 3D structures and validation plot
Peptide Sequence:
MVAERSPARSPGSWLFPGLWLLVLSGPGGLLRAQEQPSCRRAFDLYFVLDKSGSVAN
NWIEIYNFVQQLAERFVSPEMRLSFIVFSSQATIILPLTGDRGKISKGLEDLKRVSPVGET
YIEAAKKYKIYTPGANERKYNNKKPSSWEHGGYLDKVEPEKKIRTIAAYPLGVGKSASG
PGPGPKYKIYTPGANERKYGPGPGTGKRKKIRTIAAYPLGPGPGGKRKKIRTIAAYPLG
AAYKNLCFSLMDINPWLAAYIQLDKHQALRIFFLAAYSLDKDGFKVASFMLHHHHHH

Table: Final Test of Vaccine Construct

VaxiJen (Yes/No) Yes
AllerTop (Yes/No) No
ToxIBTL (Yes/No) No

Table: Physico-chemical Parameters of this Vaccine

Physicochemical Parameters Value
Number of amino acids 293
Molecular weight 32577.74
Theoretical isoelectric point (pI) 9.90
Aliphatic index 80.65
The instability index (II) 35.38
Extinction coefficient (all 51465
Cys form Cystines)

Extinction coefficients (all 51340

Cys reduced)

Total number of negatively 22

charged residues (Asp + Glu)
Total number of positively 44
charged residues (Arg + Lys)
Grand average of -0.373
hydropathicity (GRAVY)
Amino acid composition:
Secondary structure:
3D structure:

Validation plot:
 Go to procheck server
 Choose & run the file
 Click to Prockeck
 View results and click to Ramachandra Plot
 7. Scientific Journal Study

Criteria for Evaluating a journal:

 Scientific Rigor
 Editorial Quality
 Peer Review Process
 Ethics
 Publishing time
 Editiorial Board Members
 Author Rights and Copyright
 Indexing status
 Impact factor scores
 Journal operations
 Journal reputation
Explanation:
 Scientific Rigor
The scientific rigor of the articles published in the journal is a crucial
determinant of the magazine's caliber. When contemplating
publication in a new or unfamiliar journal, start by reviewing previous
years' worth of publications to evaluate information about the aim of
the study, design and methodology, data analysis, results, and
discussion—all of which can provide insight into the quality of the
research as a whole. Figures and tables should be relevant for the data,
readable, and well labeled. References must to be up to date and
thorough.
 Editorial Quality
Journal quality can be inferred from the editorial quality of
publications, especially editorials. Typing mistakes, punctuation and
grammar mistakes, or a lack of coherence and clarity in the content are
signs of inadequate editorial supervision and reviewer dedication.
These hints could indicate a journal that shouldn't be published.
 Peer Review Process
One indicator of the caliber of a journal is its transparency on the peer
review process. A respectable journal will provide a complete
description of the peer review procedure, including the standards
utilized, the reviewers chosen, the kind of review, the dates of the
review, and the editorial board's role in the process. The journal
website should also provide further information about confidentiality,
handling of conflicts of interest, and other ethical guidelines for peer
reviewers.
 Ethics
Information about plagiarism, conflicts of interest, approval from
internal review boards, informed consent, research involving human
and animal subjects, confidentiality, fraud, salami (or segmented)
publications, ghostwriting, data and image manipulation, and other
ethical issues will all be included in a high-quality journal.
 Editorial Board Members
An evaluation of a journal's editorial board can provide important
information on the caliber of the publication. Members of the editorial
board ought to be well-respected authorities in the fields relevant to
 the journal's objectives and purview, connected to reputable
organizations, and possessing the necessary scholarly qualifications.
Additionally, the editorial staff's contact details must to be included.
 Journal Reputation/Business Model
A journal's objective and scope, mission statement, publisher, and
sponsoring society organization are only a few of the factors that
contribute to its reputation. A journal's financial model should be
obvious, and if there are publication fees, they should be disclosed on
the journal website; in other words, there shouldn't be any unexpected
costs once an article is submitted for peer review.
 Author Rights and Copyright
An additional indicator of a high-quality journal is its author rights and
copyright policies. A collection of rights known as copyright grants
authors the freedom to use, distribute, show off, and alter their
creations in any format. A high-quality journal will have transparent
copyright regulations for its authors.
 Indexing Status
Authors want other people to be able to find and read their research.

Here are ten peer-reviewed journals:

 Journal of the American Chemical Society (JACS)
 PLOS Computational Biology
 Chemistry - A European Journal
 Journal of Computational Biology
 Briefings in Bioinformatics
 Journal of Biological Chemistry (JBC)
 Nature Chemical Biology
 Computational Biology and Chemistry
IEEE/ACM Transactions on Computational Biology and
Bioinformatics
 Journal of Medicinal Chemistry
Journals that publish the computational biology-related research
article:
1. Molecular plant
2. Neuro oncologuy
3. Nature cell biology
4. Journal of Computational Biology