ArticleJournal of computer-aided molecular design2010
T-Analyst: a program for efficient analysis of protein conformational changes by torsion angles.
Article in Journal of computer-aided molecular design, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 34 citations in OpenAlex.
- Mechanistic Dissection of Conformational Transition of Bicyclic Peptide via Molecular Modeling and Deep Learning.bioRxiv : the preprint server for biology · 2026Article
- CACNA1C as a Prognostic Biomarker and Therapeutic Target in High-Grade Serous Ovarian Cancer: Clinical Validation and Molecular Dynamics of Nifedipine Blockade.bioRxiv : the preprint server for biology · 2026Article
- TDTAC: a generalized time-dependent torsion angle correlation framework for resolving directional coordination in large biomolecular assemblies.Frontiers in molecular biosciences · 2026Article
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- What Strengthens Protein-Protein Interactions: Analysis and Applications of Residue Correlation Networks.Journal of molecular biology · 2023Article
- Combined ligand-based and structure-based design of PDE 9A inhibitors against Alzheimer's disease.Molecular diversity · 2022Article
- Discovery of antimicrobial agent targeting tryptophan synthase.Protein science : a publication of the Protein Society · 2022Article
- Substitution of a Surface-Exposed Residue Involved in an Allosteric Network Enhances Tryptophan Synthase Function in Cells.Frontiers in molecular biosciences · 2021Article
- Insights Into Dynamics of Inhibitor and Ubiquitin-Like Protein Binding in SARS-CoV-2 Papain-Like Protease.Frontiers in molecular biosciences · 2020Article
- Role of Molecular Interactions and Protein Rearrangement in the Dissociation Kinetics of p38α MAP Kinase Type-I/II/III Inhibitors.Journal of chemical information and modeling · 2018Article
- Engineered control of enzyme structural dynamics and function.Protein science : a publication of the Protein Society · 2018Review
- Millisecond Timescale Motions Connect Amino Acid Interaction Networks in Alpha Tryptophan Synthase.Frontiers in molecular biosciences · 2018Article
- Adaptation of a Genetic Screen Reveals an Inhibitor for Mitochondrial Protein Import Component Tim44.The Journal of biological chemistry · 2017Article
- Determinants of Macromolecular Specificity from Proteomics-Derived Peptide Substrate Data.Current protein & peptide science · 2017Review
- Characterization of Promiscuous Binding of Phosphor Ligands to Breast-Cancer-Gene 1 (BRCA1) C-Terminal (BRCT): Molecular Dynamics, Free Energy, Entropy and Inhibitor Design.PLoS computational biology · 2016Article
- Investigation of Structural Dynamics of Enzymes and Protonation States of Substrates Using Computational Tools.Catalysts (Basel, Switzerland) · 2016Article
- Achieving peptide binding specificity and promiscuity by loops: case of the forkhead-associated domain.PloS one · 2014Article
- Agonist and antagonist binding to the nuclear vitamin D receptor: dynamics, mutation effects and functional implications.In silico pharmacology · 2013Article
- The impact of Trichoderma reesei Cel7A carbohydrate binding domain mutations on its binding to a cellulose surface: a molecular dynamics free energy study.Journal of molecular modeling · 2012Article
- Mechanism of PhosphoThreonine/Serine Recognition and Specificity for Modular Domains from All-atom Molecular Dynamics.BMC biophysics · 2011Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
T-Analyst is a user-friendly computer program for analyzing trajectories from molecular modeling. Instead of using Cartesian coordinates for protein conformational analysis, T-Analyst is based on internal bond-angle-torsion coordinates in which internal torsion angle movements, such as side-chain rotations, can be easily detected. The program computes entropy and automatically detects and corrects angle periodicity to produce accurate rotameric states of dihedrals. It also clusters multiple conformations and detects dihedral rotations that contribute hinge-like motions. Correlated motions between selected dihedrals can also be observed from the correlation map. T-Analyst focuses on showing changes in protein flexibility between different states and selecting representative protein conformations for molecular docking studies. The program is provided with instructions and full source code in Perl.
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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.