Bioinformatics, ISSN 1367-4803, 11/2016, Volume 32, Issue 21, pp. 3270 - 3278
Participating as the Cornell-Gdansk group, we have used our physics-based coarsegrained UNited RESidue (UNRES) force field to predict protein structure in the...
LOCAL CONFORMATIONAL STATES | POLYPEPTIDE-CHAINS | BIOCHEMICAL RESEARCH METHODS | MOLECULAR-DYNAMICS SIMULATION | MONTE-CARLO | ALL-ATOM | POTENTIAL-ENERGY FUNCTION | UNITED-RESIDUE MODEL | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | GLOBAL OPTIMIZATION | MATHEMATICAL & COMPUTATIONAL BIOLOGY | SYSTEMS | BACKBONE | Reproducibility of Results | Animals | Protein Structure, Secondary | Humans | Models, Molecular | Protein Conformation | Proteins - chemistry | Original Papers
LOCAL CONFORMATIONAL STATES | POLYPEPTIDE-CHAINS | BIOCHEMICAL RESEARCH METHODS | MOLECULAR-DYNAMICS SIMULATION | MONTE-CARLO | ALL-ATOM | POTENTIAL-ENERGY FUNCTION | UNITED-RESIDUE MODEL | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | GLOBAL OPTIMIZATION | MATHEMATICAL & COMPUTATIONAL BIOLOGY | SYSTEMS | BACKBONE | Reproducibility of Results | Animals | Protein Structure, Secondary | Humans | Models, Molecular | Protein Conformation | Proteins - chemistry | Original Papers
Journal Article
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 9/2013, Volume 110, Issue 37, pp. 14936 - 14941
The performance of the physics-based protocol, whose main component is the United Residue (UNRES) physics-based coarse-grained force field, developed in our...
Proteins | Simulations | Databases | Chirality | Force field | Molecular dynamics | Biochemistry | Topology | Modeling | Bioinformatics | Multi-domain packing | Structure symmetry | Protein folding | multi-domain packing | TESTS | MOLECULAR-DYNAMICS | POLYPEPTIDE-CHAINS | MEAN FORCE | MULTIDISCIPLINARY SCIENCES | ALPHA | ACID SIDE-CHAINS | REPLICA EXCHANGE | PROTEIN-STRUCTURE PREDICTION | structure symmetry | UNITED-RESIDUE MODEL | protein folding | ANALYTICAL FORMULAS | Biophysical Phenomena | Humans | Models, Molecular | Protein Conformation | Protein Interaction Domains and Motifs | Proteins - chemistry | Protein Folding | Research | Biophysics | Protein-protein interactions | Biological Sciences
Proteins | Simulations | Databases | Chirality | Force field | Molecular dynamics | Biochemistry | Topology | Modeling | Bioinformatics | Multi-domain packing | Structure symmetry | Protein folding | multi-domain packing | TESTS | MOLECULAR-DYNAMICS | POLYPEPTIDE-CHAINS | MEAN FORCE | MULTIDISCIPLINARY SCIENCES | ALPHA | ACID SIDE-CHAINS | REPLICA EXCHANGE | PROTEIN-STRUCTURE PREDICTION | structure symmetry | UNITED-RESIDUE MODEL | protein folding | ANALYTICAL FORMULAS | Biophysical Phenomena | Humans | Models, Molecular | Protein Conformation | Protein Interaction Domains and Motifs | Proteins - chemistry | Protein Folding | Research | Biophysics | Protein-protein interactions | Biological Sciences
Journal Article
Journal of Molecular Modeling, ISSN 1610-2940, 8/2014, Volume 20, Issue 8, pp. 1 - 15
A unified coarse-grained model of three major classes of biological molecules—proteins, nucleic acids, and polysaccharides—has been developed. It is based on...
Proteins | Theoretical and Computational Chemistry | Chemistry | Multipole–multipole interactions | Polysaccharides | Coarse-graining | Characterization and Evaluation of Materials | Molecular Medicine | Nucleic acids | Mean-field approach | Computer Applications in Chemistry | Computer Appl. in Life Sciences | Multipole-multipole interactions | MOLECULAR-DYNAMICS | POLYPEPTIDE-CHAINS | UNRES FORCE-FIELD | POTENTIAL-ENERGY LANDSCAPE | BIOCHEMISTRY & MOLECULAR BIOLOGY | ACID SIDE-CHAINS | CHEMISTRY, MULTIDISCIPLINARY | PROTEIN-STRUCTURE PREDICTION | KNOWLEDGE-BASED POTENTIALS | COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS | BIOPHYSICS | UNITED-RESIDUE MODEL | MONTE-CARLO SIMULATIONS | ANALYTICAL FORMULAS | Macromolecular Substances - chemistry | Nucleic Acids - chemistry | Peptides - chemistry | Protein Structure, Secondary | Polysaccharides - chemistry | Protein Binding | Proteins - chemistry | Molecular Dynamics Simulation | Models | Analysis | Original Paper
Proteins | Theoretical and Computational Chemistry | Chemistry | Multipole–multipole interactions | Polysaccharides | Coarse-graining | Characterization and Evaluation of Materials | Molecular Medicine | Nucleic acids | Mean-field approach | Computer Applications in Chemistry | Computer Appl. in Life Sciences | Multipole-multipole interactions | MOLECULAR-DYNAMICS | POLYPEPTIDE-CHAINS | UNRES FORCE-FIELD | POTENTIAL-ENERGY LANDSCAPE | BIOCHEMISTRY & MOLECULAR BIOLOGY | ACID SIDE-CHAINS | CHEMISTRY, MULTIDISCIPLINARY | PROTEIN-STRUCTURE PREDICTION | KNOWLEDGE-BASED POTENTIALS | COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS | BIOPHYSICS | UNITED-RESIDUE MODEL | MONTE-CARLO SIMULATIONS | ANALYTICAL FORMULAS | Macromolecular Substances - chemistry | Nucleic Acids - chemistry | Peptides - chemistry | Protein Structure, Secondary | Polysaccharides - chemistry | Protein Binding | Proteins - chemistry | Molecular Dynamics Simulation | Models | Analysis | Original Paper
Journal Article
Letters in Organic Chemistry, ISSN 1570-1786, 2018, Volume 15, Issue 8, pp. 693 - 697
Synthesis of 1,6-anhydro sugars is well known in literature. The dioxolane ring exhibits at least two types of properties. It can be used as a protecting group...
Ac | Dioxolane ring | 1,6-anhydro derivative | Sc(OTf) | TFA/Ac | Mur-derivative | Cleavage of 1,6-anhydro linkage | dioxolane ring | Sc(OTf)/Ac2O | CELL-WALL | PEPTIDOGLYCAN | cleavage of 1,6-anhydro linkage | ESCHERICHIA-COLI | TFA/Ac2O | CHEMISTRY, ORGANIC | H2SO4/ACO | LEVOGLUCOSAN
Ac | Dioxolane ring | 1,6-anhydro derivative | Sc(OTf) | TFA/Ac | Mur-derivative | Cleavage of 1,6-anhydro linkage | dioxolane ring | Sc(OTf)/Ac2O | CELL-WALL | PEPTIDOGLYCAN | cleavage of 1,6-anhydro linkage | ESCHERICHIA-COLI | TFA/Ac2O | CHEMISTRY, ORGANIC | H2SO4/ACO | LEVOGLUCOSAN
Journal Article
JOURNAL OF PHYSICAL CHEMISTRY B, ISSN 1520-6106, 09/2019, Volume 123, Issue 37, pp. 7829 - 7839
The physics-based UNRES coarse-grained force field for the simulations of protein structure and dynamics has been extended to treat membrane proteins. The...
TESTS | MOLECULAR-DYNAMICS | ENERGY | STRUCTURE SIMULATIONS | CHEMISTRY, PHYSICAL | COOPERATIVITY | MODEL | MARTINI | CHAINS | BACKBONE | STRUCTURE PREDICTION
TESTS | MOLECULAR-DYNAMICS | ENERGY | STRUCTURE SIMULATIONS | CHEMISTRY, PHYSICAL | COOPERATIVITY | MODEL | MARTINI | CHAINS | BACKBONE | STRUCTURE PREDICTION
Journal Article
Journal of Peptide Science, ISSN 1075-2617, 02/2013, Volume 19, Issue 2, pp. 118 - 126
Journal Article
Carbohydrate Research, ISSN 0008-6215, 05/2014, Volume 389, Issue 1, pp. 154 - 164
Proper understanding of the mechanisms of binding to Gram-positive bacteria cell wall layers—especially to the peptidoglycan (PG) layer, seems to be crucial...
Conformation analysis | Peptidoglycan | Root mean square deviation | Molecular dynamic of sugar | Vancomycin derivatives | MUREIN PEPTIDOGLYCAN | CRYOELECTRON MICROSCOPY | BIOCHEMISTRY & MOLECULAR BIOLOGY | ESCHERICHIA-COLI | CELL-WALL STRUCTURE | ENTEROCOCCUS-FAECALIS | PERIPLASMIC SPACE | CHEMISTRY, ORGANIC | TERTIARY STRUCTURE | BACILLUS-SUBTILIS 168 | FORCE-FIELD | STAPHYLOCOCCUS-AUREUS | CHEMISTRY, APPLIED | Peptidoglycan - metabolism | Amino Acid Sequence | Peptidoglycan - chemistry | Glycopeptides - chemistry | Aminoglycosides - chemistry | Anti-Bacterial Agents - metabolism | Vancomycin - metabolism | Molecular Dynamics Simulation | Glycopeptides - metabolism | Vancomycin - chemistry | Aminoglycosides - metabolism | Anti-Bacterial Agents - chemistry | Vancomycin - pharmacology | Anti-Bacterial Agents - pharmacology | Aminoglycosides - pharmacology | Carbohydrate Conformation | Glycopeptides - pharmacology | Staphylococcus aureus - drug effects | Bacillus subtilis - drug effects | Bacteria | Antibacterial agents | Models
Conformation analysis | Peptidoglycan | Root mean square deviation | Molecular dynamic of sugar | Vancomycin derivatives | MUREIN PEPTIDOGLYCAN | CRYOELECTRON MICROSCOPY | BIOCHEMISTRY & MOLECULAR BIOLOGY | ESCHERICHIA-COLI | CELL-WALL STRUCTURE | ENTEROCOCCUS-FAECALIS | PERIPLASMIC SPACE | CHEMISTRY, ORGANIC | TERTIARY STRUCTURE | BACILLUS-SUBTILIS 168 | FORCE-FIELD | STAPHYLOCOCCUS-AUREUS | CHEMISTRY, APPLIED | Peptidoglycan - metabolism | Amino Acid Sequence | Peptidoglycan - chemistry | Glycopeptides - chemistry | Aminoglycosides - chemistry | Anti-Bacterial Agents - metabolism | Vancomycin - metabolism | Molecular Dynamics Simulation | Glycopeptides - metabolism | Vancomycin - chemistry | Aminoglycosides - metabolism | Anti-Bacterial Agents - chemistry | Vancomycin - pharmacology | Anti-Bacterial Agents - pharmacology | Aminoglycosides - pharmacology | Carbohydrate Conformation | Glycopeptides - pharmacology | Staphylococcus aureus - drug effects | Bacillus subtilis - drug effects | Bacteria | Antibacterial agents | Models
Journal Article
European Journal of Medicinal Chemistry, ISSN 0223-5234, 2010, Volume 45, Issue 9, pp. 4065 - 4073
In this paper we use NMR spectroscopy and molecular modeling to examine four vasopressin analogues substituted with bulky 3,3′-diphenylalanine (Dpa)...
Arginine vasopressin analogues | V 2 agonists | Simulated annealing (SA) | 3,3-Diphenylalanine enantiomers | NMR spectroscopy | Antiuterotonic activity | agonists | SYSTEM | ELUCIDATION | CHEMISTRY, MEDICINAL | TEMPERATURE-DEPENDENCE | COUPLING-CONSTANTS | ARGININE-VASOPRESSIN | SPECTROSCOPY | V-2 agonists | DYNAMICS | BINDING | DESMOPRESSIN | OXYTOCIN RECEPTORS | Amino Acid Sequence | Arginine Vasopressin - analogs & derivatives | Phenylalanine - metabolism | Magnetic Resonance Spectroscopy | Phenylalanine - analogs & derivatives | Phenylalanine - chemistry | Stereoisomerism | Models, Molecular | Arginine Vasopressin - chemistry | Protein Conformation | Executives | Peptides | Heterocyclic compounds | Analysis | Nuclear magnetic resonance spectroscopy | Models | Enantiomers | Vasopressin
Arginine vasopressin analogues | V 2 agonists | Simulated annealing (SA) | 3,3-Diphenylalanine enantiomers | NMR spectroscopy | Antiuterotonic activity | agonists | SYSTEM | ELUCIDATION | CHEMISTRY, MEDICINAL | TEMPERATURE-DEPENDENCE | COUPLING-CONSTANTS | ARGININE-VASOPRESSIN | SPECTROSCOPY | V-2 agonists | DYNAMICS | BINDING | DESMOPRESSIN | OXYTOCIN RECEPTORS | Amino Acid Sequence | Arginine Vasopressin - analogs & derivatives | Phenylalanine - metabolism | Magnetic Resonance Spectroscopy | Phenylalanine - analogs & derivatives | Phenylalanine - chemistry | Stereoisomerism | Models, Molecular | Arginine Vasopressin - chemistry | Protein Conformation | Executives | Peptides | Heterocyclic compounds | Analysis | Nuclear magnetic resonance spectroscopy | Models | Enantiomers | Vasopressin
Journal Article
Journal of Medicinal Chemistry, ISSN 0022-2623, 04/2006, Volume 49, Issue 8, pp. 2463 - 2469
In this study, four cyclic vasopressin (CYFQNCPRG-NH2, AVP) analogues substituted at positions 2 and 3 with four combinations of enantiomers of...
CHEMISTRY, MEDICINAL | DYNAMICS SIMULATION | CLONING | AUTOMATED DOCKING | RHODOPSIN | PROTEIN-COUPLED RECEPTORS | BINDING-SITE | 5-HYDROXYTRYPTAMINE(2A) RECEPTORS | AGONIST BINDING | NEUROHYPOPHYSEAL HORMONE-RECEPTORS | CONSERVED AROMATIC RESIDUES | Models, Chemical | Phenylalanine - analogs & derivatives | Stereoisomerism | Humans | Molecular Sequence Data | Structure-Activity Relationship | Vasopressins - chemistry | Receptors, Oxytocin - chemistry | Receptors, Vasopressin - chemistry | Cattle | Phenylalanine - chemistry | Computer Simulation | Imaging, Three-Dimensional | Binding Sites - drug effects | Protein Structure, Tertiary | Amino Acid Sequence | Magnetic Resonance Spectroscopy | Receptors, Oxytocin - antagonists & inhibitors | Models, Molecular | Vasopressins - pharmacology | Sequence Alignment | Animals | Ligands | Protein Conformation | Antidiuretic Hormone Receptor Antagonists | Amino Acid Substitution
CHEMISTRY, MEDICINAL | DYNAMICS SIMULATION | CLONING | AUTOMATED DOCKING | RHODOPSIN | PROTEIN-COUPLED RECEPTORS | BINDING-SITE | 5-HYDROXYTRYPTAMINE(2A) RECEPTORS | AGONIST BINDING | NEUROHYPOPHYSEAL HORMONE-RECEPTORS | CONSERVED AROMATIC RESIDUES | Models, Chemical | Phenylalanine - analogs & derivatives | Stereoisomerism | Humans | Molecular Sequence Data | Structure-Activity Relationship | Vasopressins - chemistry | Receptors, Oxytocin - chemistry | Receptors, Vasopressin - chemistry | Cattle | Phenylalanine - chemistry | Computer Simulation | Imaging, Three-Dimensional | Binding Sites - drug effects | Protein Structure, Tertiary | Amino Acid Sequence | Magnetic Resonance Spectroscopy | Receptors, Oxytocin - antagonists & inhibitors | Models, Molecular | Vasopressins - pharmacology | Sequence Alignment | Animals | Ligands | Protein Conformation | Antidiuretic Hormone Receptor Antagonists | Amino Acid Substitution
Journal Article
Journal of Peptide Science, ISSN 1075-2617, 02/2013, Volume 19, Issue 2, pp. 118 - 126
Vasopressin and oxytocin receptors belong to the superfamily of G protein‐coupled receptors and play an important role in many physiological functions. They...
vasopressin analogues | vasopressin and oxytocin receptors | receptor–ligand interactions | molecular modelling | Receptor-ligand interactions | Vasopressin and oxytocin receptors | Molecular modelling | Vasopressin analogues | CHEMISTRY, ANALYTICAL | BIOCHEMISTRY & MOLECULAR BIOLOGY | DRUG DISCOVERY | PROTEIN-COUPLED RECEPTORS | AROMATIC RESIDUES | IDENTIFICATION | receptor-ligand interactions | ARGININE-VASOPRESSIN | HORMONE | BINDING-SITE | NEPHROGENIC DIABETES-INSIPIDUS | ANTAGONISTS | EXPRESSION | Receptors, Vasopressin - chemistry | Phenylalanine - analogs & derivatives | Phenylalanine - chemistry | Humans | Molecular Docking Simulation | Vasopressins - chemistry | Receptors, Oxytocin - chemistry
vasopressin analogues | vasopressin and oxytocin receptors | receptor–ligand interactions | molecular modelling | Receptor-ligand interactions | Vasopressin and oxytocin receptors | Molecular modelling | Vasopressin analogues | CHEMISTRY, ANALYTICAL | BIOCHEMISTRY & MOLECULAR BIOLOGY | DRUG DISCOVERY | PROTEIN-COUPLED RECEPTORS | AROMATIC RESIDUES | IDENTIFICATION | receptor-ligand interactions | ARGININE-VASOPRESSIN | HORMONE | BINDING-SITE | NEPHROGENIC DIABETES-INSIPIDUS | ANTAGONISTS | EXPRESSION | Receptors, Vasopressin - chemistry | Phenylalanine - analogs & derivatives | Phenylalanine - chemistry | Humans | Molecular Docking Simulation | Vasopressins - chemistry | Receptors, Oxytocin - chemistry
Journal Article
Biopolymers, ISSN 0006-3525, 04/2006, Volume 81, Issue 5, pp. 321 - 338
The vasopressin V2 receptor (V2R) belongs to the Class A G protein–coupled receptors (GPCRs). V2R is expressed in the renal collecting duct (CD), where it...
GPCR | dDAVP | internal water | desmopressin | V2R | receptor activation | Desmopressin | Receptor activation | Internal water | RESIDUAL DIPOLAR COUPLINGS | TRANSMEMBRANE HELICES | CONSTITUTIVE ACTIVATION | BIOCHEMISTRY & MOLECULAR BIOLOGY | STRUCTURAL INSTABILITY | PROTEIN-COUPLED RECEPTORS | ANTIDIURETIC ACTIVITY | PHARMACOLOGICAL PROPERTIES | ARGININE-VASOPRESSIN | BIOPHYSICS | FUNCTIONAL EXPRESSION | NEPHROGENIC DIABETES-INSIPIDUS | Water | Biopolymers - chemistry | GTP-Binding Proteins - chemistry | Peptides - chemistry | Humans | Molecular Conformation | Models, Molecular | Phosphatidylcholines - chemistry | Deamino Arginine Vasopressin - chemistry | Receptors, Oxytocin - chemistry | Amino Acid Motifs | Receptors, Vasopressin - chemistry | Computer Simulation | Deamino Arginine Vasopressin - agonists | Conserved Sequence | Protein Binding | Ligands | Protein Conformation | Cell Membrane - metabolism | Mutation | Oxytocin - chemistry
GPCR | dDAVP | internal water | desmopressin | V2R | receptor activation | Desmopressin | Receptor activation | Internal water | RESIDUAL DIPOLAR COUPLINGS | TRANSMEMBRANE HELICES | CONSTITUTIVE ACTIVATION | BIOCHEMISTRY & MOLECULAR BIOLOGY | STRUCTURAL INSTABILITY | PROTEIN-COUPLED RECEPTORS | ANTIDIURETIC ACTIVITY | PHARMACOLOGICAL PROPERTIES | ARGININE-VASOPRESSIN | BIOPHYSICS | FUNCTIONAL EXPRESSION | NEPHROGENIC DIABETES-INSIPIDUS | Water | Biopolymers - chemistry | GTP-Binding Proteins - chemistry | Peptides - chemistry | Humans | Molecular Conformation | Models, Molecular | Phosphatidylcholines - chemistry | Deamino Arginine Vasopressin - chemistry | Receptors, Oxytocin - chemistry | Amino Acid Motifs | Receptors, Vasopressin - chemistry | Computer Simulation | Deamino Arginine Vasopressin - agonists | Conserved Sequence | Protein Binding | Ligands | Protein Conformation | Cell Membrane - metabolism | Mutation | Oxytocin - chemistry
Journal Article
Biopolymers, ISSN 0006-3525, 01/2010, Volume 93, Issue 1, pp. 47 - 60
The Escherichia coli heat shock protein ClpB, a member of the Hsp100 family, plays a crucial role in cellular thermotolerance. In co‐operation with the Hsp70...
ClpB chaperone | M domain flexibility | conformational stability | molecular dynamics | oligomer model | Molecular dynamics | Conformational stability | Oligomer model | HSP104 | MECHANISM | CRYSTAL-STRUCTURE | BIOCHEMISTRY & MOLECULAR BIOLOGY | AGGREGATED PROTEINS | DIELECTRIC MEDIUM | PROTEIN DISAGGREGATION | ATP-BINDING-SITES | SUBSTRATE-BINDING | BIOPHYSICS | N-TERMINAL DOMAIN | OLIGOMERIZATION | Endopeptidase Clp | Heat-Shock Proteins - metabolism | Adenosine Triphosphatases - metabolism | Models, Molecular | Crystallography, X-Ray | Escherichia coli Proteins - metabolism | HSP70 Heat-Shock Proteins - metabolism | Escherichia coli - metabolism | Protein Binding | Adenosine Triphosphatases - chemistry | Protein Conformation | HSP70 Heat-Shock Proteins - chemistry | Escherichia coli Proteins - chemistry | Heat-Shock Proteins - chemistry
ClpB chaperone | M domain flexibility | conformational stability | molecular dynamics | oligomer model | Molecular dynamics | Conformational stability | Oligomer model | HSP104 | MECHANISM | CRYSTAL-STRUCTURE | BIOCHEMISTRY & MOLECULAR BIOLOGY | AGGREGATED PROTEINS | DIELECTRIC MEDIUM | PROTEIN DISAGGREGATION | ATP-BINDING-SITES | SUBSTRATE-BINDING | BIOPHYSICS | N-TERMINAL DOMAIN | OLIGOMERIZATION | Endopeptidase Clp | Heat-Shock Proteins - metabolism | Adenosine Triphosphatases - metabolism | Models, Molecular | Crystallography, X-Ray | Escherichia coli Proteins - metabolism | HSP70 Heat-Shock Proteins - metabolism | Escherichia coli - metabolism | Protein Binding | Adenosine Triphosphatases - chemistry | Protein Conformation | HSP70 Heat-Shock Proteins - chemistry | Escherichia coli Proteins - chemistry | Heat-Shock Proteins - chemistry
Journal Article
Acta Biochimica Polonica, ISSN 0001-527X, 2004, Volume 51, Issue 1, pp. 129 - 136
A model for interaction of class A G protein-coupled receptor with the G protein G, segment is proposed using the rhodopsin-transducin (RD/Gt) prototype. The...
GPCR class A | Interaction | G protein | HETEROTRIMERIC G-PROTEIN | TRANSDUCIN-ALPHA | ACTIVATION | ALPHA-SUBUNIT | CRYSTAL-STRUCTURE | BIOCHEMISTRY & MOLECULAR BIOLOGY | MEMBRANES | MODEL | interaction | RHODOPSIN | BINDING | METARHODOPSIN-II
GPCR class A | Interaction | G protein | HETEROTRIMERIC G-PROTEIN | TRANSDUCIN-ALPHA | ACTIVATION | ALPHA-SUBUNIT | CRYSTAL-STRUCTURE | BIOCHEMISTRY & MOLECULAR BIOLOGY | MEMBRANES | MODEL | interaction | RHODOPSIN | BINDING | METARHODOPSIN-II
Journal Article
Journal of Molecular Graphics and Modelling, ISSN 1093-3263, 08/2018, Volume 83, pp. 92 - 99
Knowledge-based methods are, at present, the most effective ones for the prediction of protein structures; however, their results heavily depend on the...
Knowledge-based methods | Template-based restraints | Protein structure prediction | UNRES force field | Replica exchange molecular dynamics | SIDE-CHAIN | BIOCHEMISTRY & MOLECULAR BIOLOGY | BIOCHEMICAL RESEARCH METHODS | ALPHA | EXCHANGE MOLECULAR-DYNAMICS | CRYSTALLOGRAPHY | QUALITY ASSESSMENT | SPACE | COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | BACKBONE | Proteins | Molecular dynamics | File servers | Usage | Analysis
Knowledge-based methods | Template-based restraints | Protein structure prediction | UNRES force field | Replica exchange molecular dynamics | SIDE-CHAIN | BIOCHEMISTRY & MOLECULAR BIOLOGY | BIOCHEMICAL RESEARCH METHODS | ALPHA | EXCHANGE MOLECULAR-DYNAMICS | CRYSTALLOGRAPHY | QUALITY ASSESSMENT | SPACE | COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | BACKBONE | Proteins | Molecular dynamics | File servers | Usage | Analysis
Journal Article
Journal of Molecular Graphics and Modelling, ISSN 1093-3263, 11/2019, Volume 92, Issue C, pp. 154 - 166
The recent NEWCT-9P version of the coarse-grained UNRES force field for proteins, with scale-consistent formulas for the local and correlation terms, has been...
Replica-exchange molecular dynamics | Free and data-assisted modeling | protein structure prediction | Multiscale modeling | UNRES force field | TESTS | POLYPEPTIDE-CHAINS | SEARCH | BIOCHEMISTRY & MOLECULAR BIOLOGY | BIOCHEMICAL RESEARCH METHODS | CROSS-LINKING | X-RAY-SCATTERING | EXCHANGE MOLECULAR-DYNAMICS | CRYSTALLOGRAPHY | CONFORMATION | POTENTIALS | COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS | UNITED-RESIDUE MODEL | MATHEMATICAL & COMPUTATIONAL BIOLOGY | SIMULATIONS | Proteins | Molecular dynamics | Crosslinked polymers | Rankings | Analysis
Replica-exchange molecular dynamics | Free and data-assisted modeling | protein structure prediction | Multiscale modeling | UNRES force field | TESTS | POLYPEPTIDE-CHAINS | SEARCH | BIOCHEMISTRY & MOLECULAR BIOLOGY | BIOCHEMICAL RESEARCH METHODS | CROSS-LINKING | X-RAY-SCATTERING | EXCHANGE MOLECULAR-DYNAMICS | CRYSTALLOGRAPHY | CONFORMATION | POTENTIALS | COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS | UNITED-RESIDUE MODEL | MATHEMATICAL & COMPUTATIONAL BIOLOGY | SIMULATIONS | Proteins | Molecular dynamics | Crosslinked polymers | Rankings | Analysis
Journal Article
Journal of Molecular Modeling, ISSN 1610-2940, 9/2005, Volume 11, Issue 4, pp. 407 - 415
Growing evidence that rhodopsin (RD) and related G protein-coupled receptors form functional dimers/oligomers, followed by direct proof (using atomic force...
Class A | rhodopsin | Chemistry | transducin | GPCR activation | G protein | Transducin | Rhodopsin | CONTACT SITES | ALPHA-SUBUNIT | CRYSTAL-STRUCTURE | BIOCHEMISTRY & MOLECULAR BIOLOGY | DIMERIZATION | ADRENERGIC-RECEPTOR | CHEMISTRY, MULTIDISCIPLINARY | 3-DIMENSIONAL STRUCTURE | COMPLEX-FORMATION | COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS | BIOPHYSICS | PROTEIN-COUPLED RECEPTOR | class A | COVALENT CROSS-LINKING | INVERTEBRATE RHODOPSIN |
Class A | rhodopsin | Chemistry | transducin | GPCR activation | G protein | Transducin | Rhodopsin | CONTACT SITES | ALPHA-SUBUNIT | CRYSTAL-STRUCTURE | BIOCHEMISTRY & MOLECULAR BIOLOGY | DIMERIZATION | ADRENERGIC-RECEPTOR | CHEMISTRY, MULTIDISCIPLINARY | 3-DIMENSIONAL STRUCTURE | COMPLEX-FORMATION | COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS | BIOPHYSICS | PROTEIN-COUPLED RECEPTOR | class A | COVALENT CROSS-LINKING | INVERTEBRATE RHODOPSIN |