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Preprint ARTICLE | doi:10.20944/preprints202007.0144.v1

Molecular Tracing of SARS-CoV-2 in Italy in the First Three Months of the Epidemic

Alessia Lai, Annalisa Bergna, Sara Caucci, Nicola Clementi, Ilaria Vicenti, Filippo Dragoni, Anna Maria Cattelan, Stefano Menzo, Angelo Pan, Annapaola Callegaro, Adriano Tagliabracci, Arnaldo Caruso, Francesca Caccuri, Silvia Ronchiadin, Claudia Balotta, Maurizio Zazzi, Emanuela Vaccher, Massimo Clementi, Massimo Galli, Gianguglielmo Zehender

Subject: Biology And Life Sciences, Virology Keywords: phylodynamic analyses; SARS-CoV2 circulation in Italy; molecular tracing; Whole Genome Sequencing

Online: 8 July 2020 (11:00:19 CEST)

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Working Paper REVIEW

The Alterations of Cellular Signaling Pathways in the Host Cell upon the High Pathogenic Coronaviruses Infection, SARS-CoV and MERS-CoV. What Could Be Expected from the SARS-CoV-2?

Nima Hemmat, Zahra Asadzadeh, Noora Karim-ahangar, Hajar Alemohammad, Basira Najafzadeh, Afshin Derakhshani, Amir Baghbanzadeh, Hossein Bannazadeh Baghi, Darya Javadrashid, Souzan Najafi, Meriadeg Ar Gouilh, Behzad Baradaran

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; COVID-19; coronavirus; signaling pathway; molecular alteration

Online: 21 September 2020 (04:17:24 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201907.0284.v1

Inhibition of Pancreatic α-Amylase Activity by a Weight-Loss Herbal Formula RCM-107

Shiqi Luo, George Lenon, Harsharn Gill, Andrew Hung, Daniel A. Dias, Mingdi Li, Toan Linh Nguyen

Subject: Medicine And Pharmacology, Pharmacology And Toxicology Keywords: obesity; herbal medicine; molecular docking; α-amylase

Online: 25 July 2019 (08:12:19 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201902.0240.v1

Visualizing Biological Membrane Organization and Dynamics

Marc Baaden

Subject: Biology And Life Sciences, Biophysics Keywords: Molecular visualization, Lipid bilayer

Online: 26 February 2019 (12:38:17 CET)

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Preprint ARTICLE | doi:10.20944/preprints201907.0152.v1

Adjuvant Effect of Molecular Iodine in Conventional Chemotherapy for Breast Cancer. Randomized Pilot Study

Aura Moreno-Vega, Laura Vega-Riveroll, Tonatiuh Ayala, Guillermo Peralta, Jose Miguel Torres-Martel, Joel Rojas, Perla Mondragon, Adriana Dominguez, Rodrigo De Obaldia, Carlos Avecilla-Guerrero, Brenda Anguiano, Evangelina Delgado-Gonzalez, Xochitl Zambrano-Estrada, Olga Cuenca-Mico, Olivia De La Puente, Alfredo Varela-Echavarria, Carmen Aceves

Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: molecular iodine; breast cancer; chemoresistance; immune response; transcriptomic analysis

Online: 11 July 2019 (05:49:35 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202101.0473.v1

Summarize of the Available Molecular Methods for Detection of Sars-Cov-2 During the Ongoing Pandemic

Fabio Arena, Simona Pollini, Gian Maria Rossolini, Maurizio Margaglione

Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: molecular methods; virus; pandemic; Coronaviridae; COVID-19, diagnosis; UK variant; B.1.1.7 variant; 501Y.V2 variant

Online: 25 January 2021 (10:32:38 CET)

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Preprint ARTICLE | doi:10.20944/preprints202111.0329.v1

Virtual Screening with Gnina 1.0

Jocelyn Sunseri, David Koes

Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: Machine Learning; Deep Learning; Molecular Modeling; Virtual Screening; Drug Discovery

Online: 18 November 2021 (13:59:09 CET)

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Preprint ARTICLE | doi:10.20944/preprints202105.0672.v1

Unveiling the Ionic Diels-Alder Reactions within the Molecular Electron Density Theory

Luis R. Domingo, Mar Ríos-Gutiérrez, María J. Aurell

Subject: Chemistry And Materials Science, Organic Chemistry Keywords: ionic Diels-Alder reactions; Molecular Electron Density Theory; iminium cations; superelectrophiles; global electron density transfer, asynchronicity.

Online: 27 May 2021 (13:56:43 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202201.0046.v1

Veratridine Can Bind to a Site at the Mouth of the Channel Pore at Human Cardiac Sodium Channel NaV1.5

Alican Gulsevin, Andrew M Glazer, Tiffany Shields, Brett M Kroncke, Dan M Roden, Jens Meiler

Subject: Biology And Life Sciences, Biophysics Keywords: voltage-gated sodium channels; cardiac sodium channels; SCN5A; veratridine; toxins; molecular docking; Rosetta; electrophysiology; site-directed mutagenesis

Online: 5 January 2022 (18:02:52 CET)

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Preprint ARTICLE | doi:10.20944/preprints201906.0310.v1

Insights into the Diversity of Secondary Metabolites of Planktothrix Using a Biphasic Approach Combining Global Genomics and Metabolomics

Sanrda Kim Tiam, Muriel Gugger, Justine Demay, Severine Le Manach, Charlotte Duval, Cecile Bernard, Benjamin Marie

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: cyanobacteria; secondary metabolite; genome mining; molecular networking

Online: 30 June 2019 (10:42:22 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202109.0275.v1

Big Data Approach to Large Scale Molecular Dynamics Simulations: Necessity and Inevitability for Drug Design

Dheeraj Chitara, Sanjeev B. S.

Subject: Medicine And Pharmacology, Pharmacy Keywords: Cloud infrastructure; Spark; Molecular Dynamics simulations; Drug design.

Online: 16 September 2021 (11:02:38 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201804.0237.v1

Reproduction of Characteristics of Extracellular Matrices in Specific Longitudinal Depth Zone Cartilage within Spherical Organoids in Response to Changes in Osmotic Pressure

Eiichiro Takada, Shuichi Mizuno

Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: molecular profile; extracellular matrix; osmotic pressure; depth articular cartilage; spheroidal organoid; cartilage regeneration

Online: 18 April 2018 (08:48:06 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201806.0150.v1

Relative Contributions of Solubility and Mobility to the Stability of Amorphous Solid Dispersions of Poorly Soluble Drugs: A Molecular Dynamics Simulation Study

Michael Brunsteiner, Johannes Khinast, Amrit Paudel

Subject: Chemistry And Materials Science, Theoretical Chemistry Keywords: molecular dynamics simulation; amorphous; physical stability; hydrogen-bond; molecular mobility; mixing energy; molecular interactions

Online: 11 June 2018 (10:24:14 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202006.0108.v1

Comprehensive GCMS and LC-MS/MS Metabolite Profiling of Chlorella vulgaris

Hamza Ahmed Pantami, Muhammad Safwan Ahamad Bustamam, Soo Yee Lee, Intan Safinar Ismail, Siti Munirah Mohd Faudzi, Masatoshi Nakakuni, Khozirah Shaari

Subject: Chemistry And Materials Science, Organic Chemistry Keywords: Chlorella vulgaris; biodiesel; phytoremediation; molecular networking; pigments

Online: 7 June 2020 (16:36:23 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202109.0170.v1

Effects of Molecular Iodine/Chemotherapy in the Immune Component of Breast Cancer Tumoral Microenvironment

Olga Cuenca-Micó, Evangelina Delgado-González, Brenda Anguiano, Felipe Vaca-Paniagua, Alejandra Medina-Rivera, Mauricio Rodríguez-Dorantes, Carmen Aceves

Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: molecular iodine; immune response; breast cancer

Online: 9 September 2021 (10:45:34 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201806.0039.v1

Identification and Characterization of Novel Fc-Binding Heptapeptides from Experiments and Simulations

Xiaoquan Sun, Justin Weaver, Sumith Ranil Wickramasinghe, Xianghong Qian

Subject: Engineering, Bioengineering Keywords: Protein A; Heptapeptide; M13 Phage-Display; ELISA; Fc; purification; docking; molecular dynamics simulations

Online: 4 June 2018 (12:03:52 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202102.0397.v1

Molecular Docking and Biophysical Studies for Antiproliferative Assessment of Synthetic Pyrazolopyrimidinones Tethered with Hydrazide-Hydrazones

Mabrouk Horchani, Gerardo Della Sala, Alessia Caso, Federica D’Aria, Germana Esposito, Ilaria Laurenzana, Concetta Giancola, Valeria Costantino, Hichem Ben Jannet, Anis Romdhane

Subject: Chemistry And Materials Science, Analytical Chemistry Keywords: pyrazolopyrimidinone; hydrazide-hydrazone; antitumor lead compound; cytotoxic activity; antiproliferative activity; molecular docking; epidermal growth factor receptor; G-quadruplex DNA; KRAS; circular dichroism

Online: 17 February 2021 (14:05:44 CET)

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Preprint REVIEW | doi:10.20944/preprints202201.0084.v1

Yeast Hybrids in Brewing

Matthew J. Winans

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: hybrid; lager; yeast; introgression; interspecific; domestication; phylogeny; brewing; molecular; genomics

Online: 6 January 2022 (11:55:13 CET)

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Preprint ARTICLE | doi:10.20944/preprints202109.0138.v1

In-silico study of Agaricus Bisporus on DNA damaging protein

Sanket Shelke, Pravin Badhe

Subject: Medicine And Pharmacology, Pharmacy Keywords: Agaricus Bisporus; Button Mushroom; Molecular docking; PyRx software; BIOVIA Discovery studio

Online: 8 September 2021 (10:14:03 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201806.0209.v1

On Computational Aspects of Bismuth Tri-Iodide

Abaid ur Rehman Virk, Waqas Nazeer, Shin Min Kang

Subject: Computer Science And Mathematics, Computational Mathematics Keywords: topological index; Bismuth Tri-Iodide; molecular graph; Zagreb index; Randic index; zagreb polynomial

Online: 13 June 2018 (10:46:10 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201807.0085.v1

Structural Analysis of Variability and Interaction of the N-Terminal of the Oncogenic Effector CagA of Helicobacter pylori with Phosphatidylserine

Cindy P. Ulloa Guerrero, Maria del Pilar Delgado, Carlos A. Jaramillo

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: CagA; phosphatidylserine; phosphatidylserine mutations; conservation N-terminal CagA; homology modeling; molecular docking

Online: 5 July 2018 (08:34:40 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202104.0732.v1

A Real-World, Observational, Prospective Study to Assess the Molecular Epidemiology of Epidermal Growth Factor Receptor (EGFR) Mutations upon Progression on or after First-Line Therapy with a First or Second Generation EGFR Tyrosine Kinase Inhibitor in EGFR Mutation-Positive Locally Advanced or Metastatic Non-small Cell Lung Cancer: The ‘LUNGFUL’ Study

Giannis Mountzios, Anna Koumarianou, Alexandros Bokas, Dimitrios Mavroudis, Epaminondas Samantas, Evangelos Georgios Fergadis, Helena Linardou, Panagiotis Katsaounis, Elias Athanasiadis, Michalis V. Karamouzis, George Pentheroudakis, Sofia Lampaki, Marios Froudarakis, Eleni-Isidora A. Perdikouri, Alvertos Somarakis, Foteini Papageorgiou, Zoe Paparepa, Aristeidis Nikolaou, Konstantinos N. Syrigos

Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: Epidermal Growth Factor Receptor (EGFR); mutations, EGFR tyrosine kinase inhibitor; molecular epidemiology; Non-small-cell lung cancer

Online: 28 April 2021 (07:55:22 CEST)

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Preprint REVIEW | doi:10.20944/preprints202204.0067.v1

Multi-Scale Modelling of Fuel Droplet Heating and Evaporation in Combustion Engines

Jianfei Xie

Subject: Engineering, Mechanical Engineering Keywords: fuel droplet; liquid-vapour interface; molecular dynamics; evaporation coefficient; Knudsen layer; kinetic theory modelling

Online: 8 April 2022 (03:17:40 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202101.0441.v1

Andrew M. K. Nassief

Subject: Computer Science And Mathematics, Algebra And Number Theory Keywords: Quantum Similarity; DNA; Molecular Biology; Meticodes; response variance; object set reference; Bioinformatics; Computational Physics; Computational Models; Mathematics; Probability; Statistics; Comparative Modeling; Biostatics; Biostatistics

Online: 22 January 2021 (11:35:18 CET)

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Preprint ARTICLE | doi:10.20944/preprints202205.0143.v1

Immunoinformatic Guided Rational Design of a Next Generation Multi Epitope Based Peptide Vaccine against Marburg Virus Disease Combined with Molecular Docking Studies

Mujahed Mustafa, Shaza Shantier

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: Marburg virus disease (MVD); Vaccine design; Immunoinformatic; Molecular Docking Study.

Online: 10 May 2022 (14:16:20 CEST)

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Preprint REVIEW | doi:10.20944/preprints202102.0572.v1

CircRNA-Protein Interactions in Muscle Development and Diseases

Shuailong Zheng, Xujia Zhang, Emmanuel Odame, XiaoLi Xu, Yuan Chen, JiangFeng Ye, HeLin Zhou, Dinghui Dai, Bismark Kyei, Siyuan Zhan, Jiaxue Cao, jiazhong Guo, Tao Zhong, Linjie Wang, Li Li, Hongping Zhang

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: muscle; circRNA; RNA binding protein; molecular interactions; function

Online: 25 February 2021 (10:09:04 CET)

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Preprint ARTICLE | doi:10.20944/preprints201905.0364.v1

Laser-Plasma and Self-Absorption Measurements with Applications to Analysis of Atomic and Molecular Stellar Astrophysics Spectra

Christian Parigger, Christopher M Helstern, Ghaneshwar Gautam

Subject: Physical Sciences, Astronomy And Astrophysics Keywords: atomic and molecular spectroscopy; time-resolved spectroscopy; laser plasma; laser-induced optical breakdown; stellar astrophysics spectra; white dwarf stars; hydrogen; carbon Swan spectra

Online: 30 May 2019 (08:53:35 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201807.0212.v1

Optical Pumping of TeH⁺: Implications for Search for Varying m_p/m_e

Patrick R. Stollenwerk, Mark G. Kokish, Antonio G. S. de Oliveira-Filho, Fernando R. Ornellas, Brian C. Odom

Subject: Physical Sciences, Atomic And Molecular Physics Keywords: time variation of constants; proton-electron mass ratio; molecular ion; laser cooling

Online: 12 July 2018 (08:04:03 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201812.0214.v1

Effects of Selective Substitution of Cysteine Residues on the Conformational Properties of Chlorotoxin Explored by Molecular Dynamics Simulations

Andrew J. Gregory, Leah Voit-Ostricki, Sándor Lovas, Charles R. Watts

Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: αβ motif; Abu; chlorotoxin; Cys; disulfide bond; insectotoxin; isosteric substitution; L-α-aminobutyric acid; molecular dynamics; Ser

Online: 18 December 2018 (04:46:38 CET)

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Preprint ARTICLE | doi:10.20944/preprints202012.0671.v1

Modeling and Molecular Dynamics of the 3D Structure of the HPV16 E7 Protein and Its Variants

Ciresthel Bello-Rios, Sarita Montaño, Olga Lilia Garibay-Cerdenares, Lilian Esmeralda Araujo-Arcos, Marco Antonio Leyva-Vázquez, Berenice Illades-Aguiar

Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: HPV; E7; variants; molecular dynamics simulation

Online: 25 December 2020 (16:05:04 CET)

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Preprint ARTICLE | doi:10.20944/preprints201912.0212.v1

Molecular Doping for Hole Transporting Materials in Hybrid Perovskite Solar Cells

Vanira Trifiletti, Thibault Degousée, Norberto Manfredi, Oliver Fenwick, Silvia Colella, Aurora Rizzo

Subject: Chemistry And Materials Science, Nanotechnology Keywords: molecular doping; perovskite solar cell; stability; hysteresis; F4-TCNQ

Online: 16 December 2019 (07:27:35 CET)

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Preprint BRIEF REPORT | doi:10.20944/preprints202101.0416.v1

High Frequency of Viral Co-Detections in Acute Bronchiolitis

Hortense PETAT, Vincent GAJDOS, Francois ANGOULVANT, Pierre-Olivier VIDALAIN, Sandrine CORBET, Christophe MARGUET, Jacques BROUARD, Astrid VABRET, Meriadeg AR GOUILH

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Respiratory Syncytial Virus, Molecular Diagnostic, Respiratory Viruses, Coronavirus, Bronchiolitis

Online: 21 January 2021 (12:12:25 CET)

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Preprint ARTICLE | doi:10.20944/preprints202107.0687.v1

Molecular Pathogenesis and Immune Evasion of Vesicular Stomatitis Virus Inferred from Genes Expression Changes in Infected Porcine Macrophages

Lauro Velazquez-Salinas, Jessica A. Canter, James J. Zhu, Luis L. Rodriguez

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Vesicular Stomatitis Virus; macrophage; microarray analysis; differential gene expression; molecular pathogenesis; immune evasion

Online: 30 July 2021 (09:27:29 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202105.0293.v1

Effects of Amino Acid Side Chain Length and Chemical Structure on Anionic Polyglutamic and Polyaspartic Acid Cellulose-Based Polyelectrolyte Brushes

Dmitry Tolmachev, George Mamistvalov, Natalia Lukasheva, Sergey Larin, Mikko Karttunen

Subject: Chemistry And Materials Science, Biomaterials Keywords: mineralization; polyelectrolyte brushes; poly(amino acids); poly-(α,L-glutamic acid); poly-(α,L-aspartic acid); cellulose; molecular dynamics simulation.

Online: 13 May 2021 (13:09:40 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202108.0377.v1

Magnetic Field Perturbations to a Soft X-Ray Activated Fe (II) Molecular Spin State Transition

Guanhua Hao, Alpha T. N'Diaye, Thilini K. Ekanayaka, Ashley S. Dale, Xuanyuan Jiang, Esha Mishra, Corbyn Mellinger, Saeed Yazdani, John W. Freeland, Jian Zhang, Ruihua Cheng, Xiaoshan Xu, Peter A. Dowben

Subject: Physical Sciences, Condensed Matter Physics Keywords: Spin crossover; Fe(II); activation barriers; X-ray excitation; magnetic field effects; [Fe{H2B(pz)2}2(bipy)]; molecular multiferroic.

Online: 18 August 2021 (11:30:12 CEST)

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Preprint REVIEW | doi:10.20944/preprints201902.0122.v6

The Future of Leishmaniasis Treatment: Protein Targets and Beyond

Carlos A. Padilla, María J. Álvarez, Emmanuel Campo, José G. Severiche, Aldo F. Combariza

Subject: Biology And Life Sciences, Biophysics Keywords: Leishmania; Trypanosoma; Molecular Dynamics; Theoretical Chemistry

Online: 22 September 2023 (11:07:35 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201906.0140.v1

An Inactivation Switch Enables Rhythms in a Neurospora Clock Model

Abhishek Upadhyay, Michael Brunner, Hanspeter Herzel

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: circadian clock; mathematical modelling; molecular switch; Neurospora crassa; glucose compensation

Online: 15 June 2019 (14:36:50 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201907.0085.v1

Conformation and Domain Movement Analysis of Human Matrix Metalloproteinase-2: Role of Associated Zn²⁺ and Ca²⁺ Ions

Leah Voit-Ostricki, Sandor Lovas, Charles R. Watts

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: molecular dynamics; matrix metalloproteinase; domain movement; zinc binding protein; calcium binding protein

Online: 4 July 2019 (18:07:55 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202107.0564.v1

In vivo Neuropharmacological Potential of Gomphandra tetrandra (Wall.) Sleumer and in-silico Study against β-Amyloid Precursor Protein

Md Saidur Rahman, Md Nazmul Hasan Zilani, Md. Aminul Islam, Md Munaib Hasan, Md. Muzahidul Islam, Farzana Yasmin, Partha Biswas, Akinori Hirashima, Md. Ataur Rahman, Md. Nazmul Hasan, Bonglee Kim

Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: Neurological activity; GC-MS; ADMET profile; Molecular Docking; Beta-amyloid precursor protein; Alzheimer’s disease

Online: 26 July 2021 (10:27:40 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202105.0011.v1

Molecular Dynamics Simulations and MM/PBSA Analysis of Annocatacin B in ND1 Subunit of Human Mitochondrial Respiratory Complex I

Camilo Febres-Molina, Jorge A. Aguilar-Pineda, Pamela L. Gamero-Begazo, Haruna L. Barazorda-Ccahuana, Diego E. Valencia, Karin J. Vera-López, Gonzalo Dávila-Del-Carpio, Badhin Gómez

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Annocatacin B; ND1 Subunit; Mitochondrial Respiratory Complex I; MRC-I; Molecular Dynamics Simulations; MD; Hirshfeld Charges; MM/PBSA

Online: 3 May 2021 (16:13:49 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201807.0069.v1

Improvement of Performance, Stability, and Continuity by Modified Size-Consistent Multipartitioning QM/MM Method

Hiroshi C. Watanabe

Subject: Chemistry And Materials Science, Theoretical Chemistry Keywords: quantum mechanics/molecular mechanics; molecular dynamics; adaptive QM/MM; condensed matter; solvation

Online: 4 July 2018 (10:46:45 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201812.0173.v2

Synthesis, Crystal Structure, DFT studies, Docking Studies and Fluorescent Properties of 2-(Adamantan-1-yl)-2H-isoindole-1-carbonitrile

Jacques Joubert

Subject: Chemistry And Materials Science, Organic Chemistry Keywords: 2-(Adamantan-1-yl)-2H-isoindole-1-carbonitrile; X-ray diffraction; DFT; molecular orbital calculations; fluorescence; docking; nNOS; fluorescent ligand

Online: 14 December 2018 (11:41:20 CET)

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Preprint ARTICLE | doi:10.20944/preprints202006.0015.v1

Mycobacterium bovis Population Structure in Cattle and Local Badgers: Co-localisation and Variation by Farm Type

Georgina Milne, Adrian Allen, Jordon Graham, Raymond Kirke, Carl McCormick, Eleanor Presho, Robin Skuce, Andrew Byrne

Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: Bovine tuberculosis; molecular epidemiology; spatial; badgers; MLVA; Northern Ireland

Online: 3 June 2020 (09:38:28 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202102.0427.v1

A Molecular Interpretation of the Dynamics of Diffusive Mass Transport of Water Within a Glassy Polyetherimide

Andrea Correa, Antonio De Nicola, Giuseppe Scherillo, Valerio Loianno, Domenico Mallamace, Francesco Mallamace, Hiroshi Ito, Pellegrino Musto, Giuseppe Mensitieri

Subject: Chemistry And Materials Science, Biomaterials Keywords: molecular dynamics; diffusion; mass transport of water; polymer matrix

Online: 19 February 2021 (09:50:39 CET)

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Preprint ARTICLE | doi:10.20944/preprints201806.0422.v1

VALD: The Meeting Point of Data Producers and Data Users

Tatiana Ryabchikova, Yury Pakhomov, Nikolai Piskunov

Subject: Physical Sciences, Astronomy And Astrophysics Keywords: stellar spectra; atomic and molecular data; databases

Online: 26 June 2018 (13:08:52 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202109.0101.v1

Insights in the Interaction of HPV-16 E6 and Its Variants (E-G350, E-A176/G350, E-C188/G350, AAa and AAc) with MAGI-1

Lilian Esmeralda Araujo- Arcos, Ciresthel Bello-Rios, Olga Lilia Garibay- Cerdenares, Marco Antonio Leyva-Vázquez, Sarita Montaño, Berenice Illades-Aguiar

Subject: Biology And Life Sciences, Biophysics Keywords: E6; variants; MAGI-1; molecular dynamic simulation; docking

Online: 6 September 2021 (13:51:17 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201912.0281.v1

Genetic Algorithm Design of MOF-Based Gas Sensor Arrays for CO₂-in-Air Sensing

Brian A. Day, Christopher E. Wilmer

Subject: Chemistry And Materials Science, Applied Chemistry Keywords: genetic algorithms; MOFs; metal-organic frameworks; molecular modelling; arrays

Online: 21 December 2019 (10:55:20 CET)

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Working Paper ARTICLE

Calculation of the Isobaric Heat Capacities of the Liquid and Solid Phase of Organic Compounds at and around 298.15K Based on their “True” Molecular Volume

Rudolf Naef

Subject: Chemistry And Materials Science, Physical Chemistry Keywords: heat capacity; molecular volume; force-field geometry optimization; hydrocarbons; ionic liquids; siloxanes; metal complexes

Online: 29 March 2019 (08:54:23 CET)

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Preprint ARTICLE | doi:10.20944/preprints201807.0427.v1

Discovery of CNS-Like D3R- Selective Antagonists Using 3D Pharmacophore Guided Virtual Screening

Junhyung Lee, Sung Jin Cho, Mi-hyun Kim

Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: Pharmacophore; 3D-QSAR; virtual screening; D3R selective antagonist; molecular docking; CNS-like

Online: 23 July 2018 (14:09:10 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201901.0097.v1

Cavity Closure of 2-Hydroxypropyl-β-cyclodextrin: Replica Exchange Molecular Dynamics Simulations

Khanittha Kerdpol, Jintawee Kicuntod, Peter Wolschann, Seiji Mori, Chompoonut Rungnim, Manaschai Kunaseth, Hisashi Okumura, Nawee Kungwan, Thanyada Rungrotmongkol

Subject: Chemistry And Materials Science, Theoretical Chemistry Keywords: 2-Hydroxypropyl-β-cyclodextrin (HPβCD); Replica exchange molecular dynamics (REMD); Conformational change; Cavity self-closure

Online: 10 January 2019 (11:43:44 CET)

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Preprint REVIEW | doi:10.20944/preprints202112.0092.v1

Computer Simulations of Deep Eutectic Solvents. Challenges, Solutions, and Perspectives

Dmitry Tolmachev, Natalia Lukasheva, Ruslan Ramazanov, Victor Nazarychev, Natalia Borzdun, Igor Volgin, Maria Andreeva, Artyom Glova, Sofia Melnikova, Alexey Dobrovskiy, Steven A. Silber, Sergey Larin, Rafael Maglia de Souza, Mauro Carlos Costa Ribeiro, Sergey Lyulin, Mikko Karttunen

Subject: Chemistry And Materials Science, Applied Chemistry Keywords: deep eutectic solvents; computer simulation; quantum mechanics; molecular dynamics; machine leaning.

Online: 6 December 2021 (16:16:32 CET)

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Preprint REVIEW | doi:10.20944/preprints202105.0008.v1

Thermogenic Fat: Development, Physiological Function, and Therapeutic Potential

Bruna Brasil Brandão, Ankita Poojari, Atefeh Rabiee

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Adipose Tissue, Development, Molecular Circuits, Secretome, Thermogenesis, Metabolism, Obesity, Therapy

Online: 3 May 2021 (15:58:01 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202105.0348.v1

3-Methoxycarpachromene and Masticadienonic Acid as New Target Inhibitors from Pistacia atlantica Leaves against Trypanothione Reductase of Leishmania Parasites: In Vitro and In Silico Studies

Saarra Maamri, Khedidja Benarous, Mohamed Yousfi

Subject: Biology And Life Sciences, Parasitology Keywords: Pistacia atlantica leaves; L. infantum; L. major; promastigote; antileishmanial; Masticadienonic acid, 3-Methoxycarpachromene; molecular docking.

Online: 14 May 2021 (15:36:40 CEST)

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Preprint BRIEF REPORT | doi:10.20944/preprints202109.0349.v1

The Colon Transcriptome Explorer (CoTrEx) 2.0: a Reference Web-Based Resource for Exploring Population-Based Normal Colon Gene Expression

Virginia Díez-Obrero, Ferran Moratalla-Navarro, Christopher Dampier, Matthew Devall, Robert Carreras-Torres, Graham Casey, Victor Moreno

Subject: Medicine And Pharmacology, Gastroenterology And Hepatology Keywords: RNA-Seq; bioinformatics; web application; gene expression; alternative splicing; visualization; molecular epidemiology

Online: 20 September 2021 (16:56:32 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201906.0091.v1

Molecular Docking Studies of a Cyclic Octapeptide-Cyclosaplin from Sandalwood

Abheepsa Mishra, Satyahari Dey

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: apoptosis; cyclosaplin; molecular docking; protein kinases; Sandalwood

Online: 11 June 2019 (09:45:07 CEST)

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Natural products from plants such as, chemopreventive agents attract huge attention because of their low toxicity and high specificity. The rational drug design in combination with structure based modeling and rapid screening methods offer significant potential for identifying and developing lead anticancer molecules. Thus, the molecular docking method plays an important role in screening a large set of molecules based on their free binding energies and proposes structural hypotheses of how the molecules can inhibit the target. Several peptide based therapeutics have been developed to combat several health disorders including cancers, metabolic disorders, heart-related, and infectious diseases. Despite the discovery of hundreds of such therapeutic peptides however, only few peptide-based drugs have made it to the market. Moreover, until date the activities of cyclic peptides towards molecular targets such as protein kinases, proteases, and apoptosis related proteins have never been explored. In this study we explore the in silico kinase and protease inhibitor potentials of cyclosaplin as well as study the interactions of cyclosaplin with other cancer-related proteins. Previously, the structure of cyclosaplin was elucidated by molecular modeling associated with dynamics that was used in the current study. Docking studies showed strong affinity of cyclosaplin towards cancer-related proteins. The binding affinity closer to 10 indicated efficient binding. Cyclosaplin showed strong binding affinities towards protein kinases such as EGFR, VEGFR2, PKB and p38 indicating its potential role in protein kinase inhibition. Moreover, it displayed strong binding affinity to apoptosis related proteins and revealed the possible role of cyclosaplin in apoptotic cell death. The protein-ligand interactions using LigPlot displayed some similar interactions between cyclosaplin and peptide-based ligands especially in case of protein kinases and a few apoptosis related proteins. Thus, the in silico analyses gave an insight of cyclosaplin as a potential apoptosis inducer and protein kinase inhibitor.

Preprint ARTICLE | doi:10.20944/preprints202011.0047.v1

Stacking Effects on Anthraquinone/DNA Charge-Transfer Electronically Excited States

Gustavo Cárdenas, Juan J. Nogueira

Subject: Chemistry And Materials Science, Analytical Chemistry Keywords: Photodynamic Therapy; Charge Transfer; Electronically Excited States; Anthraquinone; DNA; Molecular Dynamics; TD-DFT; Transition-Density Analysis

Online: 2 November 2020 (14:15:09 CET)

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Working Paper REVIEW

Visualizing Protein Structures - Tools and Trends

Xavier Martinez, Matthieu Chavent, Marc Baaden

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: molecular graphics; protein visualization; software tools; virtual reality

Online: 12 January 2020 (16:26:54 CET)

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Preprint ARTICLE | doi:10.20944/preprints202105.0039.v1

Synthesis and Physico-Chemical Characterization of Novel Dicyclopropyl-Thiazole Compounds as Non-Toxic and Promising Antifungals

Anna Biernasiuk, Anna Banasiewicz, Maciej Masłyk, Aleksandra Martyna, Monika Janeczko, Angelika Baranowska-Łączkowska, Anna Malm, Krzysztof Z. Łączkowski

Subject: Chemistry And Materials Science, Analytical Chemistry Keywords: antifungal activity; Candida albicans; antibiofilm effect; mode of action; cytotoxicity; hemolytic assay; HOMO-LUMO; molecular electrostatic potential

Online: 5 May 2021 (12:04:01 CEST)

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Preprint REVIEW | doi:10.20944/preprints202008.0642.v1

Gigantea: Uncovering New Functions in Flower Development

Claudio Brandoli, Cesar Petri, Marcos Egea-Cortines, Julia Weiss

Subject: Biology And Life Sciences, Plant Sciences Keywords: gene ontology; molecular function; cellular localization; biological function; circadian clock; flowering time; flower development; floral scent

Online: 28 August 2020 (11:42:40 CEST)

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Preprint REVIEW | doi:10.20944/preprints202010.0041.v1

The Human Coronaviruses (HCoVs) and the Molecular Mechanisms of SARS-CoV-2 Infection

Luigi Santacroce, Ioannis A. Charitos, Domenico M. Carretta, Emanuele De Nitto, Roberto Lovero

Subject: Medicine And Pharmacology, Pulmonary And Respiratory Medicine Keywords: Coronavirus, SARS-CoV-2, Pandemics, Molecular biology, Immunity, Pathology

Online: 2 October 2020 (13:24:16 CEST)

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Preprint CONCEPT PAPER | doi:10.20944/preprints202106.0644.v1

Atoms vs. Ions: Intermediates in Reversible Electrochemical Hydrogen Evolution Reaction

Jurga Juodkazyte, Kestutis Juodkazis, Saulius Juodkazis

Subject: Chemistry And Materials Science, Analytical Chemistry Keywords: H2ER, H2OR, HER, HOR, hydrogen, hydrogen molecular ion H2+, reversible process

Online: 28 June 2021 (11:48:21 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201811.0250.v1

High-throughput of measure-preserving integrators for constant temperature molecular dynamics simulations on GPUs

Luis Guarneros-Nolasco, Ketzasmin A. Terrón-Mejía, Jorge Mulia-Rodríguez, Daniel Osorio-Gonzalez, Roberto López-Rendón, Felipe Rodriguez-Romero

Subject: Physical Sciences, Mathematical Physics Keywords: High-Throughput Molecular Dynamics (HTMD) simulations; Nosé-Hoover Chain (NHC); Canonical ensemble; Graphics Processing Units (GPUs).

Online: 9 November 2018 (15:26:49 CET)

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Preprint REVIEW | doi:10.20944/preprints202012.0700.v1

Molecular Mechanisms of Renal Progenitor Regulation: How Many Pieces in the Puzzle?

Anna Julie Peired, Maria Elena Melica, Alice Molli, Cosimo Nardi, Paola Romagnani, Laura Lasagni

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: renal progenitors; molecular mechanisms; kidney injury; single cell RNA sequencing; molecular signature

Online: 28 December 2020 (12:40:17 CET)

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Preprint ARTICLE | doi:10.20944/preprints202107.0420.v1

A Course-Based Undergraduate Research Experience on the Evolution of Antibiotic Resistance and its Molecular Basis

Katie Dickinson, Joya Mukerji, Stuart Graham, Liz Warfield, Ben Kerr

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: CURE; undergraduate research; natural selection; experimental evolution; molecular biology; genetics; structure- 46 function relationships; introductory biology; laboratory exercise

Online: 19 July 2021 (15:47:18 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202403.0096.v1

The Dual-Targeted Fusion Inhibitor Clofazimine Binds to the S2 Segment of the SARS-CoV-2 Spike Protein

Matthew R. Freidel, Pratiti A. Vakhariya, Shalinder K. Sardarni, Roger S. Armen

Subject: Medicine And Pharmacology, Medicine And Pharmacology Keywords: Clofazimine; Arbidol; Toremifene; Fusion Inhibitor; Spike-dependent; SARS-CoV-2, S2 segment; S2 subunit; Nsp13 helicase; Surface Plasmon Resonance; Molecular Docking; CHARMM

Online: 4 March 2024 (10:43:07 CET)

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Preprint REVIEW | doi:10.20944/preprints202009.0199.v1

Robust Dynamics of Synthetic Molecular Systems as A Consequence of Broken Symmetry

Yoshiyuki Kageyama

Subject: Physical Sciences, Atomic And Molecular Physics Keywords: dissipative structure; energy conversion; mechanical work; self-oscillation; collective dynamics; autonomous motion; self-replication; autocatalysis; molecular motor; molecular robot

Online: 9 September 2020 (05:24:42 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201906.0134.v1

Measurements of Gaseous Hydrogen-Nitrogen Laser-Plasma

Christian Parigger

Subject: Physical Sciences, Fluids And Plasmas Physics Keywords: atomic and molecular spectroscopy; time-resolved spectroscopy; laser plasma; laser-induced optical breakdown; stellar astrophysics spectra; white dwarf stars; hydrogen

Online: 14 June 2019 (15:01:44 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202012.0770.v2

Targeting BRF2 in Cancer Using Repurposed Drugs

Behnam Rashidieh, Maryam Molakarimi, Ammar Mohseni, Simon Tria, Sriganesh Srihari, Rachael C. Adams, Pascal H.G. Duijf, Mathew Jones, Kum Kum Khanna

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: BRF2; cancer; molecular dynamics simulation; drug repurposing; drug discovery

Online: 16 July 2021 (11:40:34 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202107.0395.v1

Melatonin/Nanoclay Hybrids for Skin Delivery

Ana Borrego-Sánchez, Daniel Muñoz-Santiburcio, César Viseras, Alfonso Hérnandez-Laguna, C. Ignacio Sainz-Díaz

Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: Melatonin; molecular modelling; adsorption; clays; modified drug release; molecular dynamics

Online: 19 July 2021 (08:44:04 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202201.0295.v1

From Water to Land: The Structural Construction and Molecular Switches in Lungs during Metamorphosis of Microhyla fissipes

Liming Chang, Meihua Zhang, Qiheng Chen, Jiongyu Liu, Wei Zhu, Jianping Jiang

Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: WGCNA; lung development; histological structure; molecular changes; amphibian

Online: 20 January 2022 (10:16:10 CET)

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Preprint ARTICLE | doi:10.20944/preprints202301.0076.v1

Molecular Docking and Dynamics Identifies Potential Repurposed Drug Candidates for COVID-19 Studies

Mohammed Muzaffar-Ur-Rehman, Chougule Suryakant, Ala Chandu, Banoth Kumar, Renuka Joshi, Snehal Jadhav, Sankaranarayanan Murugesan, Seshadri Vasan

Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: COVID-19; drug repurposing; long COVID; molecular docking; molecular dynamics; SARS-CoV-2

Online: 4 January 2023 (09:38:47 CET)

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Preprint REVIEW | doi:10.20944/preprints201907.0134.v2

Viral Infections and Autoimmune Disease: Roles of LCMV in Delineating Mechanisms of Immune Tolerance

Georgia Fousteri, Amy Dave Jhatakia

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: lymphocytic choriomeningitis virus (LCMV); viral infection; autoimmunity; molecular mimicry; bystander activation; immune tolerance

Online: 3 October 2019 (13:51:08 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202002.0062.v1

Structural Comparison of Diverse HIV-1 Subtypes using Molecular Modelling and Docking Analyses of Integrase Inhibitors

Darren Isaacs, Sello Given Mikasi, Adetayo Emmanuel Obasa, George Mondinde Ikomey, Ruben Cloete, Graeme Brandon Jacobs

Subject: Biology And Life Sciences, Virology Keywords: Integrase; HIV-1; Naturally occurring polymorphism; diversity; Molecular Modelling; Molecular Docking

Online: 5 February 2020 (11:02:15 CET)

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Preprint ARTICLE | doi:10.20944/preprints202206.0099.v1

SARS-CoV-2 Shielding Effect of Chitosan Derivatives: An in-silico Prospective

Poonam Das, Sabuj Sahoo, Sanatan Majhi, George rout Kerry, Atala Bihari Jena

Subject: Biology And Life Sciences, Virology Keywords: Chitosan; mHTCC; SARS-CoV-2; S protein; ACE2; Molecular interaction

Online: 7 June 2022 (09:05:16 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202102.0014.v1

Computational Analysis Reveals a Critical Point Mutation in the N-Terminal Region of the Signaling Lymphocytic Activation Molecule Responsible for the Cross-Species Infection with Canine Distemper Virus

Yuta Yamamoto, Shogo Nakano, Fumio Seki, Yasuteru Shigeta, Sohei Ito, Hiroaki Tokiwa, Makoto Takeda

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: canine distemper virus; signaling lymphocytic activation molecule; fragment molecular orbital calculation; molecular dynamics simulation

Online: 1 February 2021 (11:29:27 CET)

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Preprint REVIEW | doi:10.20944/preprints201812.0015.v1

Emerging Insights into the Function of Kinesin-8 Proteins in Microtubule Length Regulation

Sanjay Shrestha, Mark Hazelbaker, Amber L. Yount, Claire E. Walczak

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: microtubule dynamics; mitosis; spindle; molecular motor protein

Online: 3 December 2018 (09:06:22 CET)

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Preprint ARTICLE | doi:10.20944/preprints202107.0462.v1

Halogens in Acetophenones Direct the Hydrogen Bond Docking Preference of Phenol via Stacking Interactions

Charlotte Zimmermann, Manuel Lange, Martin A. Suhm

Subject: Chemistry And Materials Science, Analytical Chemistry Keywords: London dispersion; ketone complexes; density functional theory; hydrogen bonds; molecular recognition; vibrational spectroscopy; gas phase; benchmark

Online: 20 July 2021 (16:06:47 CEST)

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Preprint SHORT NOTE | doi:10.20944/preprints202201.0166.v1

Two Notes on the Theoretical Physics of ATP Synthase

Archit Chaturvedi

Subject: Physical Sciences, Applied Physics Keywords: Theoretical Biophysics; Mathematical Biophysics; Theoretical Biology; Molecular Biophysics

Online: 12 January 2022 (13:38:59 CET)

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Preprint ARTICLE | doi:10.20944/preprints201907.0156.v1

Spatial Molecular AlO Temperature Distributions in Laser-Induced Plasma

David M. Surmick, Daryl J. Dagel, Christian G. Parigger

Subject: Physical Sciences, Atomic And Molecular Physics Keywords: molecular spectroscopy; diatomic spectroscopy; Abel transform; plasma spectroscopy; laser-induced breakdown spectroscopy; laser-induced plasma; plasma dynamics

Online: 11 July 2019 (09:30:23 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202012.0280.v1

Process Simulation and Techno-Economic Analysis of Large-Scale Bioproduction of Sweet Protein Thaumatin II

Kirolos Kelada, Daniel Tusé, Yuri Gleba, Karen McDonald, Somen Nandi

Subject: Biology And Life Sciences, Food Science And Technology Keywords: Thaumatin, sweet protein, molecular farming, natural sweeteners

Online: 11 December 2020 (12:56:40 CET)

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Working Paper ARTICLE

Marine Bacteria from Rocas Atoll: A Promising Biotechnological Resource

Karen Y. Velasco-Alzate, Anelize Bauermeister, Marcelo M. P. Tangerina, Tito M. C. Lotufo, Marcelo J. P. Ferreira, Paula C. Jimenez, Gabriel Padilla, Norberto P. Lopes, Leticia V. Costa-Lotufo

Subject: Chemistry And Materials Science, Organic Chemistry Keywords: secondary metabolites; microbial diversity; metabolomics; molecular network; marine bacteria

Online: 19 October 2019 (02:01:18 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201808.0214.v1

3D-Printed Microfluidic Platform Enabling Bacterial Preconcentration and DNA Purification for Molecular Detection of Pathogens in Blood

Yonghee Kim, Jinyeop Lee, Sungsu Park

Subject: Chemistry And Materials Science, Analytical Chemistry Keywords: immunomagnetic separation (IMS); bacterial pathogen; 3D printing; preconcentration; DNA purification; molecular diagnostics

Online: 12 August 2018 (19:26:04 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201910.0177.v1

The Effect of Co-Doping at the A-Site on the Structure and Oxide Ion Conductivity in (Ba_0.5-xSr_x)La_0.5InO_3-δ: A Molecular Dynamics Study

Kuk-Jin Hwang, Hae-Jin Hwang, Myung-Hyund Lee, Seng-Min Jeong, Tae Ho Shin

Subject: Chemistry And Materials Science, Electrochemistry Keywords: oxide ion conductivity; perovskite oxide; molecular dynamics simulation; ceramics electrolyte

Online: 16 October 2019 (04:55:22 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202203.0328.v1

Discovery of Bispecific Lead Compounds From Azadirachta Indica Against ZIKA NS2B-NS3 Protease and RNA Dependent RNA Polymerase Using Molecular Simulations

Sanjay Kumar, Shreif A. El- Kafrawy‎, Shiv Bharadwaj, S. S. Maitra, Thamir A. Alandijany, Arwa A. Faizo, Aiah M. Khateb, Vivek Dhar Dwivedi, Esam I. Azhar

Subject: Biology And Life Sciences, Virology Keywords: Zika Virus; Flavonoids; Azadirachta indica; Molecular Docking; Molecular Dynamics Simulation; Binding free energy

Online: 24 March 2022 (09:31:59 CET)

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Preprint ARTICLE | doi:10.20944/preprints202202.0317.v1

Visualization and Comprehension of Electronic and Topographic Contrasts on Cooperatively Switched Diarylethene-Bridged Ditopic Ligand

Imen Hnid, Lihao Guan, Elarbi Chatir, Saioa Cobo, Frederic Lafolet, Francois Maurel, Jean-Christophe Lacroix, Xiaonan Sun

Subject: Chemistry And Materials Science, Nanotechnology Keywords: photochromic; diarylethene; bipyridine; high-resolution scanning tunneling microscopy; cooperative switches; molecular orbital; DFT calculations

Online: 24 February 2022 (13:17:29 CET)

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Preprint REVIEW | doi:10.20944/preprints202012.0681.v1

Understanding Root Rot Disease in Agricultural Crops

Bruce A. Williamson-Benavides, Amit Dhingra

Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: Fungi; oomycetes; resistance; susceptibility; molecular mechanisms; quantitative trait loci; mapping

Online: 28 December 2020 (11:12:35 CET)

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Preprint ARTICLE | doi:10.20944/preprints201907.0233.v1

MS-Based Approaches Enable the Structural Characterization of Transcription Factor / DNA Response Element Complex

Lukas Slavata, Josef Chmelik, Daniel Kavan, Ruzena Filandrova, Jan Fiala, Michal Rosulek, Hynek Mrazek, Zdenek Kukacka, Karel Valis, Petr Man, Michael Miller, William McIntyre, Daniele Fabris, Petr Novak

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: transcription factor; protein; DNA; protein-nucleic acid cross-linking; quantitative cross-linking; transplatin; trans-dichlorodiamineplatinum(II); hydrogen-deuterium exchange; FOXO4; molecular modeling; molecular docking

Online: 22 July 2019 (08:03:27 CEST)

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Working Paper REVIEW

Molecular Mechanisms of Chemoresistance Induced by Cisplatin in NSCLC Cancer Therapy

Jolanta Kryczka, Jakub Kryczka, Karolina Czarnecka-Chrebelska, Ewa Brzeziańska-Lasota

Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: Non–Small Cell Lung Cancer; cisplatin; chemoresistance; molecular mechanisms

Online: 14 July 2021 (11:25:13 CEST)

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Preprint REVIEW | doi:10.20944/preprints202307.0605.v1

Insight and Recommendations for Fragile X Premutation Associated Conditions from the 5th International Conference on FMR1 Premutation

Flora Tassone, Dragana Protic, Emily Allen, Alison D. Archibald, Anna Baud, W Ted Brown, Dejan B. Budimirovic, Jonathan Cohen, Brett Dufour, Rachel Eiges, Nicola Elvassore, Lidia V. Gabis, Samantha J Grudzien, Deborah Hall, David Hessl, Abigail Hogan, Jessica Ezzell Hunter, Peng Jin, Poonnada Jiraanont, Jessica Klusek, R. Frank Kooy, Claudine M Kraan, Cecilia Laterza, Andrea Lee, Karen Lipworth, Molly Losh, Danuta Z Loesch, Reymundo Lozano, Marsha Mailick, Apostolos Manolopoulos, Verónica Martínez-Cerdeño, Yingratana Amabel McLennan, Robert M. Miller, Alice Montanaro, Matthew W. Mosconi, Sarah Potter, Melissa Raspa, Susan M. Rivera, Katharine Shelly, Peter K. Todd, Katarzyna Tutak, Jun Yi Wang, Anne C Wheeler, Tri Indah Winarni, Marwa Zafarullah, Randi Hagerman

Subject: Medicine And Pharmacology, Medicine And Pharmacology Keywords: FMR1 premutation; FXPAC; FXTAS; FXAND; FXPOI; FMR1 molecular and clinical

Online: 10 July 2023 (10:27:07 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201808.0409.v3

Isolation and Characterization of Polymorphic Microsatellite loci from the Invasive Worm Branchiomma luctuosum (Grube, 1870) (Annelida: Sabellidae)

Flávia Ariany Belato, Elisa Costa-Paiva, Anderson Vilasboa

Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: bioinvasion; molecular markers; fanworm; biofouling

Online: 27 August 2018 (05:59:35 CEST)

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Preprint REVIEW | doi:10.20944/preprints202104.0339.v1

Toward an Understanding Of the Structural and Mechanistic Aspects of Protein-Protein Interactions in 2-Oxo Acid Dehydrogenase Complexes

Natalia S. Nemeria, Xu Zhang, Joao Leandro, Jieyu Zhou, Luying Yang, Sander M. Houten, Frank Jordan

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: neurodegeneration, glucose metabolism, enzyme catalysis, protein-protein interaction, hydrogen exchange mass spectrometry, protein cross-linking, protein assembly, molecular modeling

Online: 13 April 2021 (10:19:30 CEST)

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Working Paper ARTICLE

D-Amino Acid Substituted Peptides as Potential Alternatives of Homochiral L-Configurations

Jianxun Shen

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: D-amino acids; homochirality; molecular modeling; secondary structure occupancy; stability

Online: 21 January 2021 (12:44:27 CET)

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Preprint ARTICLE | doi:10.20944/preprints202306.0648.v1

Insights into the SARS-CoV-2 ORF6 Mechanism of Action

Elena Krachmarova, Peicho Petkov, Elena Lilkova, Nevena Ilieva, Miroslav Rangelov, Nadezhda Todorova, Kristina Malinova, Rossitsa Hristova, Genoveva Nacheva, Anastas Gospodinov, Leandar Litov

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: SARS-CoV-2 ORF6 – RAE1 binding; 3D molecular structure modelling; molecular dynamics simulations; cell cycle, cyclin E; R-loops; DNA replication stress

Online: 8 June 2023 (13:52:38 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202001.0372.v1

Self-assembly Synthesis of Molecularly Imprinted Polymers for the Ultrasensitive Electrochemical Determination of Testosterone

Kai-Hsi Liu, Danny O’Hare, James L. Thomas James L. Thomas, Han-Zhang Guo, Chien-Hsin Yang, Mei-Hwa Lee

Subject: Chemistry And Materials Science, Surfaces, Coatings And Films Keywords: testosterone; molecular imprinting; electronically conductive polymer; electrochemical sensing; urine.

Online: 30 January 2020 (15:06:13 CET)

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Preprint ARTICLE | doi:10.20944/preprints202204.0053.v1

Computational Investigations on the Natural Small-Molecule as an Inhibitor of Programmed Death Ligand-1 for Cancer Immunotherapy

Geethu S. Kumar, Mahmoud Moustafa, Amaresh Kumar Sahoo, Petr Malý, Shiv Bharadwaj

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Programmed death ligand-1; Natural products; Immunotherapy; Neoenactin B1; Molecular dynamics simulation

Online: 7 April 2022 (04:08:19 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202205.0349.v1

Screening and Identification of Novel Small Molecule Inhibitors against Mycobacterium tuberculosis Dihydrodipicolinate Synthase Enzyme using In Silico and In Vitro Methods

Anasuya Bhargav, Pratibha Chaurasia, Nikita V. Ivanisenko, Vladimir A. Ivanisenko, Bhupesh Taneja, Srinivasan Ramachandran

Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: Docking; lead discovery; molecular dynamic simulation; tuberculosis; coupled assay

Online: 25 May 2022 (10:11:26 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202106.0297.v1

A Functional Study of the TatD DNases of Trueperella pyogenes and the Conformational Analysis of Luteolin as an Inhibitor

Zehui Zhang, Yinfeng Liang, Lihui Yu, Menghan Chen, Yuru Guo, Zhiruo Kang, Chenghu Qu, Chunlian Tian, Dexian Zhang, Mingchun Liu

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Trueperella pyogenes; TatD DNases; luteolin; DNA hydrolysis; molecular modeling; SPR

Online: 10 June 2021 (14:13:37 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202109.0503.v1

Protein Structure, Models of Sequence Evolution, and Data Type Effects in Phylogenetic Analyses of Mitochondrial Data: A Case Study in Birds

Emily L. Gordon, Rebecca T. Kimball, Edward L. Braun

Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: mitogenome; transmembrane proteins; substitution matrix; JTT matrix; molecular evolution; partitioned models; mixture models; RY coding; cyto-nuclear discordance

Online: 29 September 2021 (16:57:38 CEST)

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Phylogenomic analyses have revolutionized the study of biodiversity, but they have revealed that estimated tree topologies can depend, at least in part, on the subset of the genome that is analyzed. For example, estimates of trees for avian orders differ if protein coding or non-coding data are analyzed. The bird tree is a good study system because the historical signal for relationships among orders is very weak, which should permit subtle non-historical signals to be identified, while monophyly of orders is strongly corroborated, allowing identification of strong non-historical signals. Hydrophobic amino acids in mitochondrially-encoded proteins, which are expected to be found in transmembrane helices, have been hypothesized to be associated with non-historical signals. We tested this hypothesis by comparing the evolution of transmembrane helices and extramembrane segments of mitochondrial proteins from 420 bird species, sampled from most avian orders. We estimated amino acids exchangeabilities for both structural environments and assessed the performance of phylogenetic analysis using each data type. We compared those relative exchangeabilities with values calculated using a substitution dataset for transmembrane helices from a variety of sampled set of nuclear- and mitochondrially-encoded proteins, allowing us to compare the bird-specific mitochondrial models with a general model of transmembrane protein evolution. To complement our amino acid analyses, we examined the impact of protein structure on patterns of nucleotide evolution. Models of transmembrane and extramembrane sequence evolution for amino acids and nucleotides exhibited striking differences, but there was no evidence for strong topological data type effects. However, incorporating protein structure into analyses of mitochondrially-encoded proteins improved model fit. Thus, we believe that considering protein structure will improve analyses of mitogenomic data, both in birds and in other taxa.

Preprint REVIEW | doi:10.20944/preprints201810.0653.v3

A Trajectory-Based Method to Explore Reaction Mechanisms

Saulo A. Vázquez, Xose L. Otero, Emilio Martinez-Nunez

Subject: Chemistry And Materials Science, Theoretical Chemistry Keywords: automated algorithm; molecular dynamics; graph theory; statistical rate theory; kinetics simulations

Online: 2 December 2018 (09:39:19 CET)

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Preprint CASE REPORT | doi:10.20944/preprints202012.0548.v1

Characterization of New ATM Deletion Associated with Hereditary Breast Cancer

Sandra Parenti, Claudio Rabacchi, Marco Marino, Elena Tenedini, Lucia Artuso, Sara Castellano, Chiara Carretta, Selene Mallia, Laura Cortesi, Angela Toss, Elena Barbieri, Rossella Manfredini, Mario Luppi, Tommaso Trenti, Enrico Tagliafico

Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: next-generation sequencing; hereditary breast cancer; Homologous Recombination Repair; hereditary cancer syndrome; Clinical genomics; Molecular diagnostics

Online: 22 December 2020 (10:17:48 CET)

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