Synthesis of Pyrrolo[3,4-b]pyridin-5-ones via Ugi–Zhu Reaction and In Vitro–In Silico Studies against Breast Carcinoma

Prospective Epigenetic Actions of Organo-Sulfur Compounds against Cancer: Perspectives and Molecular Mechanisms

(2023) Shoaib Shoaib et al.   Cancers

Uni-GBSA: an open-source and web-based automatic workflow to perform MM/GB(PB)SA calculations for virtual screening

(2023) Maohua Yang et al.   BRIEFINGS IN BIOINFORMATICS

Identification of pyrrolo[3′,4’:3,4]cyclohepta[1,2-d][1,2]oxazoles as promising new candidates for the treatment of lymphomas

(2023) Marilia Barreca et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

Combining QM/MM Calculations with Classical Mining Minima to Predict Protein–Ligand Binding Free Energy

(2023) Farzad Molani et al.   Journal of Chemical Information and Modeling

Development and test of highly accurate endpoint free energy methods. 1: Evaluation of ABCG2 charge model on solvation free energy prediction and optimization of atom radii suitable for more accurate solvation free energy prediction by the PBSA method

(2023) Yuchen Sun et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Recent Advances in Alchemical Binding Free Energy Calculations for Drug Discovery

(2023) Ingo Muegge et al.   ACS Medicinal Chemistry Letters

In-silico target prediction by ensemble chemogenomic model based on multi-scale information of chemical structures and protein sequences

(2023) Su-Qing Yang et al.   Journal of Cheminformatics

Involvement of the Orexinergic System in Cancer: Antitumor Strategies and Future Perspectives

(2023) Pilar Marcos et al.   Applied Sciences-Basel

Discovery of Potential Noncovalent Inhibitors of Dehydroquinate Dehydratase from Methicillin-Resistant Staphylococcus aureus through Computational-Driven Drug Design

(2023) César Millán-Pacheco et al.   Pharmaceuticals

Improving protein–ligand docking and screening accuracies by incorporating a scoring function correction term

(2022) Liangzhen Zheng et al.   BRIEFINGS IN BIOINFORMATICS

The method predicting interaction between protein targets and small-molecular ligands with the wide applicability domain

(2022) Dmitry A. Karasev et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

Comparative Molecular Dynamics Simulation Studies of Realistic Eukaryotic, Prokaryotic, and Archaeal Membranes

(2022) Irina D. Pogozheva et al.   Journal of Chemical Information and Modeling

PI3K Inhibitors in Advanced Breast Cancer: The Past, The Present, New Challenges and Future Perspectives

(2022) Paola Fuso et al.   Cancers

The Orexin receptors: Structural and anti-tumoral properties

(2022) Alain Couvineau et al.   Frontiers in Endocrinology

AKT1 Transcriptomic Landscape in Breast Cancer Cells

(2022) Bijesh George et al.   Cells

The New Microtubule-Targeting Agent SIX2G Induces Immunogenic Cell Death in Multiple Myeloma

(2022) Katia Grillone et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Speed vs accuracy: Effect on ligand pose accuracy of varying box size and exhaustiveness in AutoDock Vina

(2022) Rupesh Agarwal et al.   Molecular Informatics

Predicting the mutation effects of protein–ligand interactions via end-point binding free energy calculations: strategies and analyses

(2022) Yang Yu et al.   Journal of Cheminformatics

In-silico molecular modelling, MM/GBSA binding free energy and molecular dynamics simulation study of novel pyrido fused imidazo[4,5-c]quinolines as potential anti-tumor agents

(2022) Upala Dasmahapatra et al.   Frontiers in Chemistry

Current and future burden of breast cancer: Global statistics for 2020 and 2040

(2022) Melina Arnold et al.   BREAST

Nature-inspired new isoindole-based Passerini adducts as efficient tumor-selective apoptotic inducers via caspase-3/7 activation

(2022) Mohammed Salah Ayoup et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

In silico study revealed the inhibitory activity of selected phytomolecules of C. rotundus against VacA implicated in gastric ulcer

(2022) Halimat Atanda et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Molecular basis for anti-insomnia drug design from structure of lemborexant-bound orexin 2 receptor

(2022) Hidetsugu Asada et al.   STRUCTURE

2-Benzyl-3-morpholino-7-(thiophen-2-yl)-6-(thiophen-2-ylmethyl)-6,7-dihydro-5H-pyrrolo[3,4-b]pyridin-5-one

(2022) Ivette Morales-Salazar et al.   Molbank

Improving Blind Docking in DOCK6 through an Automated Preliminary Fragment Probing Strategy

(2021) Paula Jofily et al.   MOLECULES

Structures of active-state orexin receptor 2 rationalize peptide and small-molecule agonist recognition and receptor activation

(2021) Chuan Hong et al.   Nature Communications

An Effective MM/GBSA Protocol for Absolute Binding Free Energy Calculations: A Case Study on SARS-CoV-2 Spike Protein and the Human ACE2 Receptor

(2021) Negin Forouzesh et al.   MOLECULES

AKT Inhibitors: New Weapons in the Fight Against Breast Cancer?

(2021) Federica Martorana et al.   Frontiers in Pharmacology

The past, present, and future of breast cancer models for nanomedicine development

(2021) Paz Boix-Montesinos et al.   ADVANCED DRUG DELIVERY REVIEWS

AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings

(2021) Jerome Eberhardt et al.   Journal of Chemical Information and Modeling

Breast Cancer—Epidemiology, Risk Factors, Classification, Prognostic Markers, and Current Treatment Strategies—An Updated Review

(2021) Sergiusz Łukasiewicz et al.   Cancers

CHARMM-GUI Ligand Designer for Template-Based Virtual Ligand Design in a Binding Site

(2021) Hugo Guterres et al.   Journal of Chemical Information and Modeling

gmx_MMPBSA: A New Tool to Perform End-State Free Energy Calculations with GROMACS

(2021) Mario S. Valdés-Tresanco et al.   Journal of Chemical Theory and Computation

Cytotoxic and Apoptotic Effects of Chemogenic and Biogenic Nano-sulfur on Human Carcinoma Cells: A Comparative Study

(2021) Samrat Krishnappa et al.   ACS Omega

Targeting MAPK Signaling in Cancer: Mechanisms of Drug Resistance and Sensitivity

(2020) Shannon Lee et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Prospects of multitarget drug designing strategies by linking molecular docking and molecular dynamics to explore the protein–ligand recognition process

(2020) Krishnankutty Chandrika Sivakumar et al.   DRUG DEVELOPMENT RESEARCH

The Roles of Cyclin-Dependent Kinases in Cell-Cycle Progression and Therapeutic Strategies in Human Breast Cancer

(2020) Lei Ding et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Radiomics in breast cancer classification and prediction

(2020) Allegra Conti et al.   SEMINARS IN CANCER BIOLOGY

Computationally predicting binding affinity in protein–ligand complexes: free energy-based simulations and machine learning-based scoring functions

(2020) Debby D Wang et al.   BRIEFINGS IN BIOINFORMATICS

Assessing Molecular Docking Tools to Guide Targeted Drug Discovery of CD38 Inhibitors

(2020) Eric D. Boittier et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Synthesis, biological evaluation, and molecular docking analysis of phenstatin based indole linked chalcones as anticancer agents and tubulin polymerization inhibitors

(2020) Jyoti Kode et al.   BIOORGANIC CHEMISTRY

The lingering mysteries of metastatic recurrence in breast cancer

(2020) Alessandra I. Riggio et al.   BRITISH JOURNAL OF CANCER

Determinants of Orexin Receptor Binding and Activation—A Molecular Dynamics Study

(2019) Lasse Karhu et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Molecular Classification of Breast Cancer

(2019) Julia Y.S. Tsang et al.   ADVANCES IN ANATOMIC PATHOLOGY

SwissTargetPrediction: updated data and new features for efficient prediction of protein targets of small molecules

(2019) Antoine Daina et al.   NUCLEIC ACIDS RESEARCH

Accelerating Membrane Simulations with Hydrogen Mass Repartitioning

(2019) Curtis Balusek et al.   Journal of Chemical Theory and Computation

Distinct functions of AKT isoforms in breast cancer: a comprehensive review

(2019) Nico Hinz et al.   Cell Communication and Signaling

Is It Reliable to Take the Molecular Docking Top Scoring Position as the Best Solution without Considering Available Structural Data?

(2018) David Ramírez et al.   MOLECULES

ProTox-II: a webserver for the prediction of toxicity of chemicals

(2018) Priyanka Banerjee et al.   NUCLEIC ACIDS RESEARCH

SWISS-MODEL: homology modelling of protein structures and complexes

(2018) Andrew Waterhouse et al.   NUCLEIC ACIDS RESEARCH

Synthesis of polyheterocycles via multicomponent reactions

(2018) Ilich A. Ibarra et al.   ORGANIC & BIOMOLECULAR CHEMISTRY

Evaluation of Cytotoxic Potentials of Some Isoindole-1,3-Dione Derivatives on HeLa, C6 and A549 Cancer Cell Lines

(2018) Ayse Tan et al.   Medicinal Chemistry

Investigation of New Orexin 2 Receptor Modulators Using In Silico and In Vitro Methods

(2018) Jana Janockova et al.   MOLECULES

CHARMM-GUI ligand reader and modeler for CHARMM force field generation of small molecules

(2017) Seonghoon Kim et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

GPCRdb in 2018: adding GPCR structure models and ligands

(2017) Gáspár Pándy-Szekeres et al.   NUCLEIC ACIDS RESEARCH

SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules

(2017) Antoine Daina et al.   Scientific Reports

CHARMM-GUI Input Generator for NAMD, Gromacs, Amber, Openmm, and CHARMM/OpenMM Simulations using the CHARMM36 Additive Force Field

(2016) Jumin Lee et al.   BIOPHYSICAL JOURNAL

Discovery of 3-(3-(4-(1-Aminocyclobutyl)phenyl)-5-phenyl-3H-imidazo[4,5-b]pyridin-2-yl)pyridin-2-amine (ARQ 092): An Orally Bioavailable, Selective, and Potent Allosteric AKT Inhibitor

(2016) Jean-Marc Lapierre et al.   JOURNAL OF MEDICINAL CHEMISTRY

Geometrical structure, potentiometric, molecular docking and thermodynamic studies of azo dye ligand and its metal complexes

(2016) A.A. El-Bindary et al.   JOURNAL OF MOLECULAR LIQUIDS

CHARMM36m: an improved force field for folded and intrinsically disordered proteins

(2016) Jing Huang et al.   NATURE METHODS

Design and Synthesis of Non-Peptide, Selective Orexin Receptor 2 Agonists

(2015) Takashi Nagahara et al.   JOURNAL OF MEDICINAL CHEMISTRY

PASS Targets: Ligand-based multi-target computational system based on a public data and naïve Bayes approach

(2015) P.V. Pogodin et al.   SAR AND QSAR IN ENVIRONMENTAL RESEARCH

CHARMM-GUIMembrane Buildertoward realistic biological membrane simulations

(2014) Emilia L. Wu et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Lipid Organization of the Plasma Membrane

(2014) Helgi I. Ingólfsson et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The chemistry of isoindole natural products

(2013) Klaus Speck et al.   Beilstein Journal of Organic Chemistry

Toward an Understanding of Agonist Binding to Human Orexin-1 and Orexin-2 Receptors with G-Protein-Coupled Receptor Modeling and Site-Directed Mutagenesis

(2013) Alexander Heifetz et al.   BIOCHEMISTRY

MMPBSA.py: An Efficient Program for End-State Free Energy Calculations

(2012) Bill R. Miller et al.   Journal of Chemical Theory and Computation

MDAnalysis: A toolkit for the analysis of molecular dynamics simulations

(2011) Naveen Michaud-Agrawal et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

BSP-SLIM: A blind low-resolution ligand-protein docking approach using predicted protein structures

(2011) Hui Sun Lee et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Orexin 2 receptor as a potential target for immunotoxin and antibody-drug conjugate cancer therapy

(2011) MASATO KISHIDA et al.   Oncology Letters

Assessing the Performance of the MM/PBSA and MM/GBSA Methods. 1. The Accuracy of Binding Free Energy Calculations Based on Molecular Dynamics Simulations

(2010) Tingjun Hou et al.   Journal of Chemical Information and Modeling

Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: Four approaches that performed well in CASP8

(2009) Elmar Krieger et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

CHARMM-GUI: A web-based graphical user interface for CHARMM

(2008) Sunhwan Jo et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY