FlexPortal
FlexPortal integrates computational methods and databases for macromolecular flexibility analysis, supporting molecular dynamics simulations, conformational transition tracing, docking/QSAR, and genomic DNA structural and chromatin dynamics analyses.
Key Features:
- Molecular Dynamics Simulations: Incorporates MDWeb and MDMoby for access to standard and high-throughput MD workflows, supports system preparation from PDB structures, and runs Amber, NAMD, and Gromacs with trajectory analysis via the MoDEL database.
- Conformational Transition Analysis: Implements GOdMD (Gō-like Discrete Molecular Dynamics) using discrete molecular dynamics engines combined with enhanced sampling methods including metadynamics, Maxwell Demon MD, and essential dynamics to trace complex non-linear transitions without chemical distortion.
- Docking and QSAR Integration: Provides SEABED functionality for receptor preparation, library editing, flexible ensemble docking, hybrid docking/QSAR experiments, and virtual screening on protein mutants.
- Genomic DNA Analysis: Incorporates DNAlive for graphical and quantitative analysis of structural and physical properties of genomic DNA, derivation of 3D information from large naked and protein-bound sequences, and a mesoscopic Metropolis code for chromatin fiber dynamics with integration of protein and genomic databases.
- Pathway Estimation for Conformational Transitions: Implements MDdMD (Molecular Dynamics Discrete Molecular Dynamics) combining essential dynamics with Maxwell-Demon sampling to estimate transition pathways at multiple resolutions including atomistic.
Scientific Applications:
- Protein conformational analysis: Analysis and tracing of protein conformational transitions and dynamic behavior using GOdMD, MDdMD, and MD simulations.
- Molecular dynamics simulation and trajectory analysis: Generation and analysis of MD trajectories with Amber, NAMD, and Gromacs and subsequent trajectory mining via the MoDEL database for standard and high-throughput studies.
- Docking, QSAR, and virtual screening: Receptor preparation, flexible ensemble docking, hybrid docking/QSAR workflows, and virtual screening of protein mutants using SEABED.
- Genomic DNA structure and chromatin dynamics: Derivation of 3D structural information for large DNA sequences and study of chromatin fiber dynamics using DNAlive and a mesoscopic Metropolis code.
- Pathway estimation and enhanced sampling: Estimation of conformational pathways and enhanced sampling using essential dynamics, metadynamics, and Maxwell Demon MD.
Methodology:
Integration of discrete molecular dynamics engines (GOdMD, MDdMD) with enhanced sampling strategies (metadynamics, Maxwell Demon MD, essential dynamics); use of Amber, NAMD, and Gromacs; system preparation from PDB structures; trajectory analysis via the MoDEL database; DNAlive analysis and a mesoscopic Metropolis code for chromatin fibers.
Topics
Collections
Details
- Maturity:
- Mature
- Cost:
- Free of charge
- Tool Type:
- workflow
- Operating Systems:
- Linux
- Programming Languages:
- PHP, JavaScript, Python
- Added:
- 9/30/2016
- Last Updated:
- 11/25/2024
Operations
Data Inputs & Outputs
Data retrieval
Outputs
Publications
Sfriso P, Hospital A, Emperador A, Orozco M. Exploration of conformational transition pathways from coarse-grained simulations. Bioinformatics. 2013;29(16):1980-1986. doi:10.1093/bioinformatics/btt324. PMID:23740746.
Fenollosa C, Otón M, Andrio P, Cortés J, Orozco M, Goñi JR. SEABED: Small molEcule activity scanner weB servicE baseD. Bioinformatics. 2014;31(5):773-775. doi:10.1093/bioinformatics/btu709. PMID:25348211. PMCID:PMC7297214.
Goñi JR, Fenollosa C, Pérez A, Torrents D, Orozco M. DNAlive: a tool for the physical analysis of DNA at the genomic scale. Bioinformatics. 2008;24(15):1731-1732. doi:10.1093/bioinformatics/btn259. PMID:18544548.
Hospital A, Andrio P, Fenollosa C, Cicin-Sain D, Orozco M, Gelpí JL. MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations. Bioinformatics. 2012;28(9):1278-1279. doi:10.1093/bioinformatics/bts139. PMID:22437851.
Meyer T, D'Abramo M, Hospital A, Rueda M, Ferrer-Costa C, Pérez A, Carrillo O, Camps J, Fenollosa C, Repchevsky D, Gelpí JL, Orozco M. MoDEL (Molecular Dynamics Extended Library): A Database of Atomistic Molecular Dynamics Trajectories. Structure. 2010;18(11):1399-1409. doi:10.1016/j.str.2010.07.013. PMID:21070939.
Camps J, Carrillo O, Emperador A, Orellana L, Hospital A, Rueda M, Cicin-Sain D, D'Abramo M, Gelpí JL, Orozco M. FlexServ: an integrated tool for the analysis of protein flexibility. Bioinformatics. 2009;25(13):1709-1710. doi:10.1093/bioinformatics/btp304. PMID:19429600.
Hospital A, Faustino I, Collepardo-Guevara R, González C, Gelpí JL, Orozco M. NAFlex: a web server for the study of nucleic acid flexibility. Nucleic Acids Research. 2013;41(W1):W47-W55. doi:10.1093/nar/gkt378. PMID:23685436. PMCID:PMC3692121.
Hospital A, Andrio P, Cugnasco C, Codo L, Becerra Y, Dans PD, Battistini F, Torres J, Goñi R, Orozco M, Gelpí JL. BIGNASim: a NoSQL database structure and analysis portal for nucleic acids simulation data. Nucleic Acids Research. 2015;44(D1):D272-D278. doi:10.1093/nar/gkv1301. PMID:26612862. PMCID:PMC4702913.
Sfriso P, Emperador A, Orellana L, Hospital A, Gelpí JL, Orozco M. Finding Conformational Transition Pathways from Discrete Molecular Dynamics Simulations. Journal of Chemical Theory and Computation. 2012;8(11):4707-4718. doi:10.1021/ct300494q. PMID:26605625.