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Search results for: PROTEIN STRUCTURE PREDICTION, MULTISCALE MODELING, UNRES FORCE FIELD, FREE AND BIOINFORMATICS-ASSISTED MODELING, REPLICA-EXCHANGE MOLECULAR DYNAMICS
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Prediction of Protein Structure by Template-Based Modeling Combined with the UNRES Force Field
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Protein structure prediction with the UNRES force-field using Replica-Exchange Monte Carlo-with-Minimization; Comparison with MCM, CSA, and CFMC
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Application of Multiplexed Replica Exchange Molecular Dynamics to the UNRES Force Field: Tests with α and α+β Proteins
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Explicit solvent repulsive scaling replica exchange molecular dynamics ( RS‐REMD ) in molecular modeling of protein‐glycosaminoglycan complexes
PublicationGlycosaminoglcyans (GAGs), linear anionic periodic polysaccharides, are crucial for many biologically relevant functions in the extracellular matrix. By interacting with proteins GAGs mediate processes such as cancer development, cell proliferation and the onset of neurodegenerative diseases. Despite this eminent importance of GAGs, they still represent a limited focus for the computational community in comparison to other classes...
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Modeling the Structure, Dynamics, and Transformations of Proteins with the UNRES Force Field
PublicationThe physics-based united-residue (UNRES) model of proteins ( www.unres.pl ) has been designed to carry out large-scale simulations of protein folding. The force field has been derived and parameterized based on the principles of statistical-mechanics, which makes it independent of structural databases and applicable to treat nonstandard situations such as, proteins that contain D-amino-acid residues. Powered by Langevin dynamics...
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Modeling protein structures with the coarse-grained UNRES force field in the CASP14 experiment
PublicationThe UNited RESidue (UNRES) force field was tested in the 14th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP14), in which larger oligomeric and multimeric targets were present compared to previous editions. Three prediction modes were tested (i) ab initio (the UNRES group), (ii) contact-assisted (the UNRES- contact group), and (iii) template-assisted (the UNRES-template...
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A coarse‐grained approach to NMR ‐data‐assisted modeling of protein structures
PublicationThe ESCASA algorithm for analytical estimation of proton positions from coarse-grained geometry developed in our recent work has been implemented in modeling protein structures with the highly coarse-grained UNRES model of polypeptide chains (two sites per residue) and nuclear magnetic resonance (NMR) data. A penalty function with the shape of intersecting gorges was applied to treat ambiguous distance restraints, which automatically...
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Improvements and new functionalities of UNRES server for coarse-grained modeling of protein structure, dynamics, and interactions
PublicationIn this paper we report the improvements and extensions of the UNRES server (https://unres-server.chem.ug.edu.pl) for physics-based simulations with the coarse-grained UNRES model of polypeptide chains. The improvements include the replacement of the old code with the recently optimized one and adding the recent scale-consistent variant of the UNRES force field, which performs better in the modeling of proteins with the β and the...
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Improved Consensus-Fragment Selection in Template-Assisted Prediction of Protein Structures with the UNRES Force Field in CASP13
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Simulation of Protein Structure and Dynamics with the Coarse-Grained UNRES Force Field
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Prediction of protein structure with the coarse-grained UNRES force field assisted by small X-ray scattering data and knowledge-based information
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Investigation of Protein Folding by Coarse-Grained Molecular Dynamics with the UNRES Force Field
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A Hierarchical Multiscale Approach to Protein Structure Prediction: Production of Low‐Resolution Packing Arrangements of Helices and Refinement of the Best Models with a United‐Residue Force Field
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Evaluation of the scale-consistent UNRES force field in template-free prediction of protein structures in the CASP13 experiment
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Replica Exchange and Multicanonical Algorithms with the Coarse-Grained United-Residue (UNRES) Force Field
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JOURNAL OF MOLECULAR MODELING
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UNRES-Dock—protein–protein and peptide–protein docking by coarse-grained replica-exchange MD simulations
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Performance of protein-structure predictions with the physics-based UNRES force field in CASP11
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Use of Restraints from Consensus Fragments of Multiple Server Models To Enhance Protein-Structure Prediction Capability of the UNRES Force Field
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Implementation of a Serial Replica Exchange Method in a Physics-Based United-Residue (UNRES) Force Field
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