Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Drug Discovery: Overview01:26

Drug Discovery: Overview

10.4K
Drug discovery is a multifaceted process involving extensive screening, testing, and optimization of lead compounds to identify potential new drugs for therapeutic use. It combines several approaches, including screening large numbers of natural products, chemical modification of known active molecules, identification of new drug targets, and rational design based on biological mechanisms and drug-receptor structure. These approaches are carried out in both academic research laboratories and...
10.4K
Pharmacodynamic Models: Overview01:27

Pharmacodynamic Models: Overview

159
Pharmacodynamic (PD) responses describe the interaction between a drug and its biological target, culminating in a physiological effect. These responses can be classified into different types: continuous variables, such as blood glucose levels; categorical outcomes, like survival rates; and time-to-event metrics, such as disease progression. Understanding and modeling PD responses are critical for optimizing drug efficacy and safety.PD models describe the relationship between drug concentration...
159
Pharmacodynamics: Overview and Principles01:21

Pharmacodynamics: Overview and Principles

3.9K
Pharmacodynamics is a scientific field that delves into drugs' intricate biochemical, cellular, and physiological effects on the human body. The study of pharmacodynamics helps us understand how drugs interact with the body and elicit various responses.
Most drugs' effects result from their interactions with drug receptors or targets within the body. These interactions trigger specific responses at the cellular or systemic level. Drug receptors can be found on the surfaces of cells or...
3.9K
Pharmacogenomics: Identification of New Drug Targets01:29

Pharmacogenomics: Identification of New Drug Targets

121
Advances in genomics have profoundly influenced drug discovery by increasing both the speed and accuracy of pharmaceutical development. Pharmacogenomics, which examines how genetic variation influences drug response, facilitates the identification of novel therapeutic targets and enables patient stratification for personalized treatment. These strategies contribute to improved drug efficacy, minimized adverse effects, and more efficient clinical trial design.Mapping genetic differences...
121
Pharmacokinetic–Pharmacodynamic Relationship: Problems01:24

Pharmacokinetic–Pharmacodynamic Relationship: Problems

127
The empirical approach to drug therapy optimization relies on correlating pharmacological response with administered dosage. Such an approach can be costly, time-consuming, and often yields poor correlation due to variables like formulation factors and drug elimination characteristics. A more precise approach correlates response with plasma drug concentration or the amount of drug in the body, rather than dosage. This is achieved through pharmacokinetic-pharmacodynamic (PK/PD) modeling, which...
127
Pharmacodynamic Models: Emax Drug–Concentration Effect Model01:18

Pharmacodynamic Models: Emax Drug–Concentration Effect Model

240
The Emax drug-concentration effect model is central to pharmacodynamics in drug discovery and development. This model is predicated on the receptor occupancy theory, which posits that the effect of a drug is directly related to the number of receptors occupied by the drug and the resultant complex formation.The model describes the reversible interaction between a drug (C) and a receptor (R) to form a drug-receptor complex (RC). The kinetics of this interaction are quantified by an equation that...
240

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Developing ribose fatty acid mono-esters as novel oleogelators with tailored colloidal properties: enzymatic synthesis, structure-activity relationships and mechanistic insights.

Journal of colloid and interface science·2026
Same author

Functionalized carbon fiber cloth for the disposable sensor in robust nonenzymatic glucose detection.

Talanta·2026
Same author

Virological characteristics of SARS-CoV-2-related coronaviruses dynamically circulating in Southeast Asia.

Cell·2026
Same author

New Analogs of the Compstatin Family of Clinical Complement Inhibitors with Low Picomolar Target Affinity.

Journal of medicinal chemistry·2026
Same author

Species-specific roles of SP1 in bovine and human embryonic genome activation and early embryonic development.

Proceedings of the National Academy of Sciences of the United States of America·2026
Same author

Molecular diagnosis of maturity-onset diabetes of the young via whole-exome sequencing: a cohort study in Taizhou, China.

Endocrine·2026
Same journal

Multimodal feature fusion for molecular property classification.

Journal of cheminformatics·2026
Same journal

P2MAT: A machine learning (ML) driven software for Property Prediction of MATerial.

Journal of cheminformatics·2026
Same journal

Computational design of low-volatility lubricants for space using interpretable machine learning.

Journal of cheminformatics·2026
Same journal

OpenStats: how to combine statistics and research data management (RDM) to leverage efficient scientific data analysis by guided statistics.

Journal of cheminformatics·2026
Same journal

Unified heterogeneity-aware benchmark of drug synergy prediction: a cross-study analysis of traditional machine learning and graph deep learning models.

Journal of cheminformatics·2026
Same journal

Count your bits: fingerprint benchmarking to assess broad chemical space representation.

Journal of cheminformatics·2026
See all related articles

Related Experiment Video

Updated: May 1, 2026

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
08:49

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Published on: June 20, 2025

1.6K

PharmDock: a pharmacophore-based docking program.

Bingjie Hu1, Markus A Lill1

  • 1Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, IN 47906, USA.

Journal of Cheminformatics
|April 18, 2014
PubMed
Summary
This summary is machine-generated.

PharmDock, a new protein pharmacophore-based docking program, integrates pose sampling and ranking for improved ligand pose prediction and binding affinity estimation. It offers superior performance and user-guided features for drug discovery.

Keywords:
Biased dockingConfined dockingConstraint dockingDockingGUIProtein pharmacophoresPyMOLScoring

More Related Videos

Network Pharmacology Prediction and Metabolomics Validation of the Mechanism of Fructus Phyllanthi against Hyperlipidemia
11:06

Network Pharmacology Prediction and Metabolomics Validation of the Mechanism of Fructus Phyllanthi against Hyperlipidemia

Published on: April 7, 2023

2.9K
Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

1.3K

Related Experiment Videos

Last Updated: May 1, 2026

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
08:49

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Published on: June 20, 2025

1.6K
Network Pharmacology Prediction and Metabolomics Validation of the Mechanism of Fructus Phyllanthi against Hyperlipidemia
11:06

Network Pharmacology Prediction and Metabolomics Validation of the Mechanism of Fructus Phyllanthi against Hyperlipidemia

Published on: April 7, 2023

2.9K
Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

1.3K

Area of Science:

  • Computational chemistry
  • Structural biology
  • Drug discovery

Background:

  • Protein-based pharmacophore models capture ligand-protein interactions.
  • Previous work demonstrated their utility in ligand pose prediction and ranking.
  • Existing docking programs can be enhanced with pharmacophore information.

Purpose of the Study:

  • Introduce PharmDock, a novel pharmacophore-based docking program.
  • Combine optimized protein-based pharmacophore models with empirical scoring for docking.
  • Evaluate PharmDock's performance against established docking tools.

Main Methods:

  • Developed PharmDock integrating pharmacophore-based pose sampling, ranking, and local optimization.
  • Utilized optimized protein-based pharmacophore models.
  • Incorporated user-defined guidance features based on experimental data.

Main Results:

  • PharmDock demonstrated comparable or superior performance in ligand pose prediction, binding affinity estimation, compound ranking, and virtual screening.
  • User-guided docking significantly outperformed unbiased docking.
  • The program includes an intuitive GUI within PyMOL.

Conclusions:

  • PharmDock is a novel protein pharmacophore-based docking program.
  • It offers enhanced performance and flexibility for drug discovery applications.
  • PharmDock and its PyMOL plugin are freely accessible.