ArticlePLoS computational biology2010
Conformational transitions upon ligand binding: holo-structure prediction from apo conformations.
Article in PLoS computational biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
50 citing papers in PubMed.
- Integrated In Silico Analysis Reveals ABC Transporter ATP-Binding Protein as a Therapeutic Target inACS omega · 2026Article
- In-Depth Molecular Dynamics Simulations Reveal Ligand-Induced Modulations of the HSPA8-SARS-CoV-2 Spike Protein Interaction.International journal of molecular sciences · 2026Article
- Molecular docking and dynamics reveal novel CDK6 inhibitors for targeted glioblastoma therapy.Scientific reports · 2026Article
- Integrative in vitro and in silico evaluation of HSP60-derived peptides as immunomodulators of the TLR4/MD-2 complex.Scientific reports · 2025Article
- In vitro investigation of Datura innoxia phytocompounds against Mycobacterium tuberculosis H37Ra strain in association with in silico studies.Scientific reports · 2025Article
- ColdstartCPI: Induced-fit theory-guided DTI predictive model with improved generalization performance.Nature communications · 2025Article
- A combined in silico and MD simulation approach to discover novel LpxC inhibitors targeting multiple drug resistant Pseudomonas aeruginosa.Scientific reports · 2025Article
- Statistical Thermodynamics of the Protein Ensemble: Mediating Function and Evolution.Annual review of biophysics · 2025Review
- Anthelmintic Potential and In Silico Studies of Ricinoleic Acid from the Seed Oil ofInternational journal of molecular sciences · 2025Article
- Elucidation of α-glucosidase inhibitory activity and UHPLC-ESI-QTOF-MS based metabolic profiling of endophytic fungiFrontiers in fungal biology · 2025Article
- AlphaFold2-Based Characterization of Apo and Holo Protein Structures and Conformational Ensembles Using Randomized Alanine Sequence Scanning Adaptation: Capturing Shared Signature Dynamics and Ligand-Induced Conformational Changes.International journal of molecular sciences · 2024Article
- Investigating the Molecular Interactions of Quinoline Derivatives for Antibacterial Activity Against Bacillus subtilis: Computational Biology and In Vitro Study Interpretations.Molecular biotechnology · 2024Article
- Efficient Refinement of Complex Structures of Flexible Histone Peptides Using Post-Docking Molecular Dynamics Protocols.International journal of molecular sciences · 2024Article
- ATP-dependent conformational dynamics in a photoactivated adenylate cyclase revealed by fluorescence spectroscopy and small-angle X-ray scattering.Communications biology · 2024Article
- Antidepressant-Like Activity and Molecular Docking Analysis of a Sesquiterpene Lactone Isolated from the Root Bark ofEvidence-based complementary and alternative medicine : eCAM · 2024Review
- The role of solvation on the conformational landscape of α-synuclein.The Analyst · 2023Article
- In silico drug repurposing for coronavirus (COVID-19): screening known HCV drugs against the SARS-CoV-2 spike protein bound to angiotensin-converting enzyme 2 (ACE2) (6M0J).Molecular diversity · 2023Article
- Extensive Sampling of Molecular Dynamics Simulations to Identify Reliable Protein Structures for Optimized Virtual Screening Studies: The Case of the hTRPM8 Channel.International journal of molecular sciences · 2022Article
- Enhanced Conformational Sampling with an Adaptive Coarse-Grained Elastic Network Model Using Short-Time All-Atom Molecular Dynamics.Journal of chemical theory and computation · 2022Article
- Computational screening of camostat and related compounds against human TMPRSS2: A potential treatment of COVID-19.Saudi pharmaceutical journal : SPJ : the official publication of the Saudi Pharmaceutical Society · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Biological function of proteins is frequently associated with the formation of complexes with small-molecule ligands. Experimental structure determination of such complexes at atomic resolution, however, can be time-consuming and costly. Computational methods for structure prediction of protein/ligand complexes, particularly docking, are as yet restricted by their limited consideration of receptor flexibility, rendering them not applicable for predicting protein/ligand complexes if large conformational changes of the receptor upon ligand binding are involved. Accurate receptor models in the ligand-bound state (holo structures), however, are a prerequisite for successful structure-based drug design. Hence, if only an unbound (apo) structure is available distinct from the ligand-bound conformation, structure-based drug design is severely limited. We present a method to predict the structure of protein/ligand complexes based solely on the apo structure, the ligand and the radius of gyration of the holo structure. The method is applied to ten cases in which proteins undergo structural rearrangements of up to 7.1 A backbone RMSD upon ligand binding. In all cases, receptor models within 1.6 A backbone RMSD to the target were predicted and close-to-native ligand binding poses were obtained for 8 of 10 cases in the top-ranked complex models. A protocol is presented that is expected to enable structure modeling of protein/ligand complexes and structure-based drug design for cases where crystal structures of ligand-bound conformations are not available.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.