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marcius's protein_structure [86 articles]

 
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From The Cover: Global mapping of the protein structure space and application in structure-based inference of protein function
 
Recent advances in the development and application of implicit solvent models in biomolecule simulations.
 
Effective energy functions for protein structure prediction.
 
Empirical force fields for biological macromolecules: overview and issues.
 
Force fields for protein simulations.
 
Thermodynamics of protein folding: a microscopic view.
 
Choosing SNPs Using Feature Selection.
 
Structural characterization of proteins using residue environments.
 
Assigning new GO annotations to protein data bank sequences by combining structure and sequence homology.
 
The RCSB PDB information portal for structural genomics.
 
Crystal structure of TM1367 from Thermotoga maritima at 1.90 A resolution reveals an atypical member of the cyclophilin (peptidylprolyl isomerase) fold.
 
Crystal structure of a glycerate kinase (TM1585) from Thermotoga maritima at 2.70 A resolution reveals a new fold.
 
Structural biologyProteins downhill all the way
 
Atom-by-atom analysis of global downhill protein folding
 
How different amino acid sequences determine similar protein structures: The structure and evolutionary dynamics of the globins
 
PDB-UF: database of predicted enzymatic functions for unannotated protein structures from structural genomics.
 
High-resolution protein folding with a transferable potential
 
The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling
 
Residue-rotamer-reduction algorithm for the protein side-chain conformation problem
 
'Protein Peeling': an approach for splitting a 3D protein structure into compact fragments
 
Grow to Fit Molecular Dynamics (G2FMD): an ab initio method for protein side-chain assignment and refinement
 
Knowledge-based potential functions in protein design.
 
Prediction of protein thermostability with a direction- and distance-dependent knowledge-based potential.
 
PMUT: a web-based tool for the annotation of pathological mutations on proteins.
 
Characterization of disease-associated single amino acid polymorphisms in terms of sequence and structure properties.
 
The SWISS-MODEL Repository: new features and functionalities.
 
Evolutionary information for specifying a protein fold
 
The evolution of protein structures.
 
A tour of structural genomics
 
Protein Structure Prediction: Inroads to Biology
 
Improvement in protein functional site prediction by distinguishing structural and functional constraints on protein family evolution using computational design.
 
Structural similarity to bridge sequence space: finding new families on the bridges.
 
Fragnostic: walking through protein structure space.
 
How do side chains orient globally in protein structures?
 
Comparative molecular dynamics-Similar folds and similar motions?
 
Protein loop structure prediction with flexible stem geometries.
 
Assessment of predictions submitted for the CASP6 comparative modelling category.
 
Prediction of novel and analogous folds using fragment assembly and fold recognition.
 
SPARKS 2 and SP(3) servers in CASP 6.
 
Evaluating the usefulness of protein structure models for molecular replacement.
 
Improvement of comparative model accuracy by free-energy optimization along principal components of natural structural variation.
 
Structure prediction of membrane proteins.
 
State-of-the-art in membrane protein prediction.
 
Hamiltonians for protein tertiary structure prediction based on three-dimensional environment principles.
 
Computational analysis of alpha-helical membrane protein structure: implications for the prediction of 3D structural models.
 
Assembly of a polytopic membrane protein structure from the solution structures of overlapping peptide fragments of bacteriorhodopsin.
 
Protein complexes: structure prediction challenges for the 21(st) century.
 
Recoverable one-dimensional encoding of protein three-dimensional structures.
 
PROTEIN REFINEMENT: A NEW CHALLENGE FOR CASP IN ITS 10TH ANNIVERSARY
 
Empirical limits for template-based protein structure prediction: the CASP5 example.
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