Log in

Relevant bibliographies by topics / PyMol Viewer / Journal articles

To see the other types of publications on this topic, follow the link: PyMol Viewer.

Journal articles on the topic 'PyMol Viewer'

Author: Grafiati

Published: 7 June 2025

Last updated: 2 August 2025

Create a spot-on reference in APA, MLA, Chicago, Harvard, and other styles

Select a source type:

Consult the top 24 journal articles for your research on the topic 'PyMol Viewer.'

Next to every source in the list of references, there is an 'Add to bibliography' button. Press on it, and we will generate automatically the bibliographic reference to the chosen work in the citation style you need: APA, MLA, Harvard, Chicago, Vancouver, etc.

You can also download the full text of the academic publication as pdf and read online its abstract whenever available in the metadata.

Browse journal articles on a wide variety of disciplines and organise your bibliography correctly.

1

Lua, Rhonald C., and Olivier Lichtarge. "PyETV: a PyMOL evolutionary trace viewer to analyze functional site predictions in protein complexes." Bioinformatics 26, no. 23 (2010): 2981–82. http://dx.doi.org/10.1093/bioinformatics/btq566.

Full text

APA, Harvard, Vancouver, ISO, and other styles

2

S, Sujatha, and Rajini R. "In-Silico Enactment of Musa paradisiaca (L.) Exudate Against the Urotlithiatic Disease by Docking Study." Indian Journal of Science and Technology 17, no. 28 (2024): 2889–96. https://doi.org/10.17485/IJST/v17i28.1899.

Full text

Abstract:

Abstract <strong>Objectives:</strong> Urolithiasis is a condition that occurs when the stones exit the renal pelvis and move onto the remainder of the urinary collecting system. Musa paradisiaca (L.) is a plant with high nutritive value and has been used for the treatment of various diseases including urolithiasis. The objective of the present study was designed to detect the receptor-ligand binding energy and interaction through a molecular docking from the bio-active compounds in an exudates of M. paradisiaca pseudo stem on urolithiatic causative protein named as glycolate oxidase recep

APA, Harvard, Vancouver, ISO, and other styles

3

Sujatha, S., and R. Rajini. "In-Silico Enactment of Musa paradisiaca (L.) Exudate Against the Urotlithiatic Disease by Docking Study." Indian Journal Of Science And Technology 17, no. 28 (2024): 2889–96. http://dx.doi.org/10.17485/ijst/v17i28.1899.

Full text

Abstract:

Objectives: Urolithiasis is a condition that occurs when the stones exit the renal pelvis and move onto the remainder of the urinary collecting system. Musa paradisiaca (L.) is a plant with high nutritive value and has been used for the treatment of various diseases including urolithiasis. The objective of the present study was designed to detect the receptor-ligand binding energy and interaction through a molecular docking from the bio-active compounds in an exudates of M. paradisiaca pseudo stem on urolithiatic causative protein named as glycolate oxidase receptor (PDB ID: 2RDU). Methods: In

APA, Harvard, Vancouver, ISO, and other styles

4

Mohd., Azyumardi Azra. "A Setting Technique for Comparative Protein Modelling for Web based SMART Tool." Applied Science and Biotechnology Journal for Advanced Research 3, no. 1 (2024): 21–25. https://doi.org/10.5281/zenodo.10691316.

Full text

Abstract:

When the "hairless protein" linked to the hairless gene, which is necessary for hair growth, stops working, the result will be total hairlessness. This gene is located on chromosome 8 at locations 22027873-22045326. The hairless gene, which similarly aids in histone demethylation, is a member of the JmjC domain superfamily. With 1189 residues in the hairless protein, the domain sequence spans positions 946 to 1157 and is 212 amino acids long. JmjC domains have been identified in over 100 bacterial and eukaryotic sequences due to significant sequence similarity. Among them the human hairless ge

APA, Harvard, Vancouver, ISO, and other styles

5

Malki, Esam. "Structural studies on azadirachtin targeting the glucuronosyltransferase from lymphatic filariasis and its inhibition." Majmaah Journal of Health Sciences 12, no. 2 (2024): 69. http://dx.doi.org/10.5455/mjhs.2024.02.008.

Full text

Abstract:

Background and Aims: Brugia malayi, Brugia timori, and Wuchereria bancrofti are parasitic worms that cause lymphatic filariasis, also known as elephantiasis in some parts of the world. Because no effective vaccines and current treatments have adverse pharmacological properties, this condition has sparked much interest in the drug discovery community. This research aims to assess the efficacy of azadirachtin against a possible therapeutic target, intestine glucuronosyltransferase protein, in treating and preventing lymphatic filariasis. Methods: I-Tasser was used to create the protein, Uniprot

APA, Harvard, Vancouver, ISO, and other styles

6

Wischmeyer, Joshua, Christine Baird, Julian Grandvallet Contreras, Alexander Tran, Tsu Phang, and Marilyn Manco-Johnson. "A Novel Factor VIII Mutation with Increased Activity, Severe Thrombosis and Resistance to Activated Protein C." Blood 144, Supplement 1 (2024): 135. https://doi.org/10.1182/blood-2024-202202.

Full text

Abstract:

Background: An 18-year-old male presented with recurrent, life-threatening thromboses since birth including arterial (perinatal stroke, splenic infarct) and venous (bilateral lower extremity, mesenteric vein, portal vein and pulmonary emboli). He was found to have markedly elevated factor VIII (FVIII) activity ranging from 300 to 900%. Objective: The objective of this study was to investigate this abnormal FVIII function and structure. Methods: Assays performed included: prothrombin time (PT)/international normalized ratio (INR), activated partial thromboplastin time (aPTT), fibrinogen, comple

APA, Harvard, Vancouver, ISO, and other styles

7

Majolagbe, Olusola Nathaniel, Felicia Oguntunji, Ezekiel Gbadebo Adeyeni, Yetunde Mutiat Feruke-Bello, and Louis Odinakose Ezediuno. "Synthesis and Determination of Antimicrobial Efficacies of Secondary Metabolite of Streptomyces longisporoflavus and its 3D-Protein Structural Prediction." Journal of Advances in Medical and Pharmaceutical Sciences 25, no. 3 (2023): 20–30. http://dx.doi.org/10.9734/jamps/2023/v25i3605.

Full text

Abstract:

Aims: The need for new drug molecules is of high significance considering the rate at which pathogenic bacteria evolve into drug-resistant pathogens. Actinomycetes have been reported as valuable biological agents that possess potent bioactive molecules. This work aims to isolate local strains of actinomycetes in the environment and determine their antimicrobial activities against some clinical isolates. Study Design: This was an in-vitro study. Place and Duration of Study: The research was carried out at the Microbial Resources Research Laboratory, Department of Pure and Applied Bi

APA, Harvard, Vancouver, ISO, and other styles

8

Ezediuno, Louis Odinakaose, Michael Asebake Ockiya, Luqman Oluwaseun Awoniyi, Adeola Oyepeju Sangodare, Kehinde Busuyi David, and Faith Owabhel Robert. "Developing cancer vaccine with carcinoembryonic antigen and IGF-1R as immunostimulants using immunoinformatics approach." Korean Journal of Clinical Oncology 21, no. 1 (2025): 20–31. https://doi.org/10.14216/kjco.24326.

Full text

Abstract:

Purpose: Colorectal cancer (CRC) remains a significant global health burden, necessitating innovative approaches for prevention and treatment. This study proposes a multiepitope vaccine targeting carcinoembryonic antigen (CEA) and insulin-like growth factor-1 receptor (IGF-1R), two prominent biomarkers associated with CRC progression.Methods: Sequences of CEA and IGF-1R proteins were retrieved from NCBI databank, the sequences were aligned on the MEGA5 tool to identify conserved regions. Immunological and structural predictive analysis which include antigenic potential prediction, cytotoxic T-

APA, Harvard, Vancouver, ISO, and other styles

9

Mittal, Payal, Aritri Chowdhury, and Girish Chandra Arya. "An Insight into Absorption, Distribution, Metabolism, Excretion, and Toxicity Screening, Molecular Dynamic Simulation, and Molecular Docking of Glycitein as Hepatoprotective Isoflavone." Asian Journal of Pharmaceutical Research and Health Care 16, no. 2 (2024): 124–37. http://dx.doi.org/10.4103/ajprhc.ajprhc_76_23.

Full text

Abstract:

ABSTRACT Background: Several chemicals and metals, as well as a number of pharmaceutical preparations, are reportedly thought to have a major impact on the emergence of liver disease. According to postcommercialization regulatory considerations, it has been regarded as the most predisposing factor for acute liver failure. Thus, according to recent statistics, nearly 1 in 10 people have a liver illness of some form. 5.5 million of them suffer from chronic liver disease. Any type of viral infection, immune system abnormalities, ingestion of too many poisons, cancer, or other genetic condition ma

APA, Harvard, Vancouver, ISO, and other styles

10

Janson, Giacomo, and Alessandro Paiardini. "PyMod 3: a complete suite for structural bioinformatics in PyMOL." Bioinformatics, October 3, 2020. http://dx.doi.org/10.1093/bioinformatics/btaa849.

Full text

Abstract:

Abstract Summary The PyMod project is designed to act as a fully integrated interface between the popular molecular graphics viewer PyMOL, and some of the most frequently used tools for structural bioinformatics, e.g. BLAST, HMMER, Clustal, MUSCLE, PSIPRED, DOPE and MODELLER. Here we report its latest release, PyMod 3, which has been completely renewed with a graphical interface written in PyQt, to make it compatible with the most recent PyMOL versions, and has been extended with a large set of new functionalities compared to its predecessor, i.e. PyMod 2. Starting from the amino acid sequence

APA, Harvard, Vancouver, ISO, and other styles

11

M, Guruvigneshwari, Vijaya Bharathi R, Radha R, and Sooriyapriya B. "In silico Inhibition studies of constituents of Abutilon indicum on Xanthine oxidase." Research Journal of Pharmacy and Technology, March 24, 2022, 1133–36. http://dx.doi.org/10.52711/0974-360x.2022.00190.

Full text

Abstract:

Objective: To find out the xanthine oxidase inhibitory potential of constituents reported from the Abutilon indicum through in silico studies as there is traditional claim supporting the use of this plant in treating gout. Method: The 33 constituents of Abutilon indicum were chosen for the study and their drug likeness were read using online application SwissADME. Molecular docking studies were done in Autodock version 1.5.6. The docked samples were viewed using Molegro Molecular Viewer 2.5.0. and Pymol. Allopurinol was used as standard to compare the docking scores of the plant constituents.

APA, Harvard, Vancouver, ISO, and other styles

12

Farajnia, Safar, Zahra Shadman, Samaneh Ghasemali, et al. "In silico Validation of Pseudomonas aeruginosa Exotoxin A Domain I Interaction with the Novel Human scFv Antibody." Infectious Disorders - Drug Targets 23 (March 29, 2023). http://dx.doi.org/10.2174/1871526523666230329104537.

Full text

Abstract:

Background:: Pseudomonas(P.) aeruginosa is one of the leading causes of nosocomial infections. The pathogenicity of P. aeruginosa is related to its inherent antimicrobial resistance and the diverse virulence factors of this bacterium. Owing to the specific role of exotoxin A in P. aeruginosa pathogenesis, it is known as a promising therapeutic candidate to develop antibodies as an alternative to antibiotics. Objective:: The present study aimed to validate the interaction between a single-chain fragment variable (scFv) antibody identified from an scFv phage library against domain I exotoxin A b

APA, Harvard, Vancouver, ISO, and other styles

13

K., NAGALAKSHMI, SHILA S., INBATHAMIZH L., THENMOZHI A., RASAPPAN P., and SRINIVASAN P. T. "TARGETING NUCLEAR FACTOR KAPPA B WITH CHELATED ZINC COMPOUNDS TOWARDS ANTICANCER DRUG DESIGN." International Journal of Applied Pharmaceutics, July 7, 2021, 123–27. http://dx.doi.org/10.22159/ijap.2021v13i4.41650.

Full text

Abstract:

Objective: The objective of the study was to analyse the target-ligand interactions between nuclear factor-κB (NF-κB) and chelated Zinc compounds and to explore the anticancer drug potential of these ligands by a bio computational approach. Methods: Bioinformatics databases and tools were applied for the study. Three dimensional structure of the target NF-κB was retrieved from Protein Data Bank (PDB). The optimized structures of two chelated Zinc compounds, Zinc acetate and Zinc orotate were taken for docking studies with the target using docking tool AutoDock 4.2. Drug properties of the

APA, Harvard, Vancouver, ISO, and other styles

14

"Computer-aided Evaluation of Anti-SARS-CoV-2 (3-chymotrypsin-like Protease and Transmembrane Protease Serine 2 Inhibitors) Activity of Cepharanthine: An In silico Approach." Biointerface Research in Applied Chemistry 12, no. 1 (2021): 768–80. http://dx.doi.org/10.33263/briac121.768780.

Full text

Abstract:

3-chymotrypsin-like protease (3CLPRO) is found in severe acute respiratory syndrome coronavirus (SARS CoV)-2, and transmembrane protease serine 2 (TMPRSS-2) in humans, both of them have a role in viral attachment and proliferation. 3CLPRO and TMPRSS-2 are the most vital target for the discovery of an anti-corona virus. One efficient approach used to screen potential active compounds against specific target proteins, such as 3CLPRO and TMPRSS-2, is molecular docking. Cepharanthine (CEP) exhibits antiviral activity in SARS-CoV at 9.5 µg/mL IC50 level. This study aims to perform an in silico stud

APA, Harvard, Vancouver, ISO, and other styles

15

YERRAKULA, GOUTHAM, SAMUEL GIDEON GEORGE, KRISHNA KUMAR D., ANAND VIJAYA KUMAR P. R., JAWAHAR N., and SENTHIL VENKATACHALAM. "EFFECT OF NON-SYNONYMOUS SINGLE-NUCLEOTIDE POLYMORPHISM OF HUMAN CARBOXYL ESTERASE 1 ON THE BIOACTIVATION OF DABIGATRAN ETEXILATE." International Journal of Applied Pharmaceutics, September 7, 2022, 208–13. http://dx.doi.org/10.22159/ijap.2022v14i5.44682.

Full text

Abstract:

Objective: Dabigatran Etexilate is an oral acting direct thrombin inhibitor used for prophylaxis of cardioembolic events in non-valvular atrial fibrillation patients. Genetic polymorphisms in hCES1 gene can significantly alter the conformations of the enzyme drug binding and impair the catalytic ability. Hence this study is performed to determine the effect of single nucleotide variations on dabigatran activation by hCES1. Methods: Energy minimization was performing using YASARA server. Dihedral angles of the modeled targets were visualized using Ramachandran Plot. We performed molecular docki

APA, Harvard, Vancouver, ISO, and other styles

16

Zhang, Haiyue, Yiling Hu, Dongli Pan, Yuehua Xv, and Weifeng Shen. "Genetic Analysis of a Pedigree With Antithrombin and Prothrombin Compound Mutations and Antithrombin Heterozygotes." Frontiers in Genetics 13 (April 4, 2022). http://dx.doi.org/10.3389/fgene.2022.832582.

Full text

Abstract:

Background and Aims: Antithrombin (AT) is the most important physiological inhibitor in vivo, and coagulation factor II (FII) or prothrombin is a coagulation factor vital to life. The purpose of our research was to illustrate the connection between gene mutations and the corresponding deficiencies of AT and FII.Methods: Functional and molecular analyses were performed. The possible impact of the mutation was analyzed by online bioinformatics software. ClustalX-2.1-win and PyMol/Swiss-Pdb Viewer software were used for conservative analyses and to generate molecular graphic images, respectively.

APA, Harvard, Vancouver, ISO, and other styles

17

V., Nagalakshmi, Lavanya J., Bhavya B., Riya V., Venugopal B., and Ramesh A. Sai. "In-silico Profiling of Deleterious Non Synonymous SNPs of Homogentisate 1, 2 Dioxygenase (HGD) Gene for Early Diagnosis of “Alkaptonuria”." Research Journal of Pharmacy and Technology, September 28, 2022, 3898–904. http://dx.doi.org/10.52711/0974-360x.2022.00653.

Full text

Abstract:

In-silico characterization and molecular modelling of a single amino acid substitution in HGD (Homogentisate 1,2dioxygenase) gene are mainly caused by the deficiency of enzyme Homogentisate 1,2dioxygenase (HGD). An enzyme HGD involved in the catabolism of amino acids such as tyrosine and phenylalanine. The objective of this study was to analyse non-synonymous SNPs from highly deleterious missense mutations which affect the protein function of HGD gene. Based on 3D structure different computational algorithms were performed to identify deleterious SNPs and assess the influence of mutation by us

APA, Harvard, Vancouver, ISO, and other styles

18

Dongerdiye, Rashmi, Sujatha Jagadeesh, Beena Suresh, et al. "Novel pathogenic variant c.2714C>A (p. Thr905Lys) in the HK1 gene causing severe haemolytic anaemia with developmental delay in an Indian family." Journal of Clinical Pathology, December 25, 2020, jclinpath—2020–206960. http://dx.doi.org/10.1136/jclinpath-2020-206960.

Full text

Abstract:

Hexokinase (EC 2.7.1.1, Adenosine Tri Phosphate (ATP): D-hexose-6-phosphotransferase) is a crucial regulatory enzyme of the glycolytic pathway (Embden-Meyerhof pathway). Hexokinase deficiency is associated with chronic non-spherocytic haemolytic anaemia (HA) with some exceptional cases showing psychomotor/mental retardation and fetus death. The proband is a four-and-half-year-old female child born of a four-degree consanguineous marriage hailing from South India with autosomal recessive congenital HA associated with developmental delay. She was well till 3 months of her age post an episode of

APA, Harvard, Vancouver, ISO, and other styles

19

C, Benedict Paul, Sheshadri S. Temkar, Amruta Sridhara, et al. "Potential Aromatase Inhibitors from Centella asiatica with Non-synonymous SNPs - A Computational Approach." Current Computer-Aided Drug Design 19 (May 25, 2023). http://dx.doi.org/10.2174/1573409919666230525151933.

Full text

Abstract:

Background: Aromatase Inhibitors are used in the treatment of breast cancer as they are effective in decreasing the concentration of estrogen. As SNPs impact the efficacy or toxicity of drugs, evaluating them with mutated conformations would help in identifying potential inhibitors. In recent years, phytocompounds have been under scrutiny for their activity as potential inhibitors. Objective: In this study, we have evaluated Centella asiatica compounds for their activity on aromatase with clinically significant SNPs: rs700519, rs78310315 and rs56658716. Methods: Using AMDock v.1.5.2, which use

APA, Harvard, Vancouver, ISO, and other styles

20

Huiqing, Li, Wang Zhiqing, Jia Hui, Wei Jing, Dong Youming та Yu Zhiyue. "Interaction between N-phenyl-1-naphthylamine and β-lactoglobulin / N-fenil-1-naftilamin and β-laktoglobulin arasındaki etkileşim". Turkish Journal of Biochemistry 41, № 1 (2016). http://dx.doi.org/10.1515/tjb-2016-0003.

Full text

Abstract:

AbstractObjective: We aimed to explore the interaction between hydrophobic molecule N-phenyl-1-naphthylamine (AN) and major bovine milk protein β-lactoglobulin (β-LG) in aqueous solution.Methods: We use a combination of experiment and theoretical calculation to study how the β-lactoglobulin and AN interact. Fluorescence spectra were recorded on an F-4500 fluorescence spectrometer. The absorption spectra of AN were recorded on a 2250 UV-vis spectrophotometer. The crystal structure of β-LG (1B0O) is obtained from Protein Data Bank. Molecular docking was carried out using the AutoDock4.2 software

APA, Harvard, Vancouver, ISO, and other styles

21

Donakonda, Madhuri, Srija Indrakanti, Praveen Kumar Pasala, Malleswari Desari, and Shireesha Kammari. "A rapid RP-HPLC method for the simultaneous estimation of Ivacaftor and Tezacaftor and in silico study of their metabolitic products." Future Journal of Pharmaceutical Sciences 7, no. 1 (2021). http://dx.doi.org/10.1186/s43094-021-00254-y.

Full text

Abstract:

Abstract Background This study was designed to develop a reliable method for estimation of Ivacaftor and Tezacaftor in pure and its pharmaceutical dosage form by RP-HPLC in human plasma. Molecular docking studies were carried out and the results were visualized using PyMol and Discovery studio visualizer (Discovery studio visualizer ver. 2.5). The pharmacokinetic properties such as Swiss ADME and pKCSM of the Ivacaftor and its metabolites Ivacaftor M1, M6 and Tezacaftor and metabolites Tezacaftor M1, M2 were predicted. In admetSAR, web-based query tools incorporating a molecular built-in inter

APA, Harvard, Vancouver, ISO, and other styles

22

Roy, Matrika Saha, Rehnuma Tanjin, Tanmoy Debnath, et al. "In silico assessment of chronic toxicity of a combination drug namely ‘Olmesartan medoxomil and Hydrochlorothiazide’, marketed in Bangladesh." Future Journal of Pharmaceutical Sciences 7, no. 1 (2021). http://dx.doi.org/10.1186/s43094-021-00388-z.

Full text

Abstract:

Abstract Background Nowadays combination therapy has become more popular due to their additional effect, synergistic effect and antagonistic effect. Any of these can influence the treatment profile. Combination therapy is used to treat some chronic diseases like diabetes, hypertension, cancer etc. But recently India has banned some fixed dose drug combinations due to their increased chances of adverse drug effects and drug interactions. So it is the time to take a look on the present drug combinations available in Bangladesh. An in silico study may provide important information about their pro

APA, Harvard, Vancouver, ISO, and other styles

23

Elengoe, Asita, and Nishalini Devi Sundramoorthy. "Molecular Docking of Curcumin With Breast Cancer Cell Line Proteins." Pharmaceutical and Biomedical Research, June 28, 2020. http://dx.doi.org/10.18502/pbr.v6i1.3425.

Full text

Abstract:

Background: Breast cancer is known as the most widely recognized dangerous tumors; therefore, the most common reason for mortality among all instances of harmful neoplastic illness in females. This is because the lack of specific signs and symptoms at the early stage and at the aggressive nature. Currently, breast cancer treatment such as chemotherapy, surgery and radiotherapy has not been effective. Objectives: In this study, Three-Dimensional (3D) structures of caspase 3, mucosal addressin cell adhesion molecule 1 (MADCAM1) and nuclear factor NF-kappa-B-p105 subunit (breast cancer cell

APA, Harvard, Vancouver, ISO, and other styles

24

Barros, Adriana Rolim Campos, Marina de Barros Mamede Vidal Damasceno, Sacha Aubrey Alves Rodrigues Santos, et al. "TRPV1 Mediates The Orofacial Antinociceptive Effect of Frutalin: In Vivo and In Silico Studies." FASEB Journal 31, S1 (2017). http://dx.doi.org/10.1096/fasebj.31.1_supplement.812.6.

Full text

Abstract:

Our previous studies have shown the orofacial antinociceptive effect of frutalin (FTL) and it was suggested that FTL effect on acute orofacial pain could be mediated by TRPA1 and TRPV1. Docking study indicated that FTL strongly interacts with TRPV1. This study was conducted to investigate the relationship between TRPV1/TRPA1 channels and the orofacial antinociceptive effect of FTL. Mice (n=6/group) were pretreated with vehicle (0.9 % NaCl; 10 mL/kg; i.p.), FTL (0.5 mg/kg; i.p.), ruthenium red (TRPV1 antagonist, 3 mg/kg, s.c.) or camphor (TRPA1 antagonist, 7.6 mg/kg, s.c.) 30 min before injecti

APA, Harvard, Vancouver, ISO, and other styles

We offer discounts on all premium plans for authors whose works are included in thematic literature selections. Contact us to get a unique promo code!