Optimization of solvation models for predicting the structure of surface loops in proteins

scientific article published on 01 May 2001

Optimization of solvation models for predicting the structure of surface loops in proteins is …
instance of (P31):
scholarly articleQ13442814

External links are
P356DOI10.1002/PROT.1041
P698PubMed publication ID11288180

P2093author name stringB Das
H Meirovitch
P2860cites workAccessible surface areas as a measure of the thermodynamic parameters of hydration of peptidesQ24610354
Canonical structures for the hypervariable regions of immunoglobulinsQ69450418
Multiple conformational states of proteins: a molecular dynamics analysis of myoglobinQ69706390
Prediction of the folding of short polypeptide segments by uniform conformational samplingQ69715633
Mechanisms of antibody binding to a proteinQ69766097
The inclusion of electrostatic hydration energies in molecular mechanics calculationsQ70233002
A critical assessment of comparative molecular modeling of tertiary structures of proteinsQ71267484
The importance of being floppyQ72347273
Ab initio prediction of the solution structures and populations of a cyclic pentapeptide in DMSO based on an implicit solvation modelQ73595085
On the transferability of atomic solvation parameters: Ab initio structural prediction of cyclic heptapeptides in DMSOQ74199456
Prediction of loop geometries using a generalized born model of solvation effectsQ77386247
Packing structures and transitions in liquids and solidsQ81031838
Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic LiquidsQ99192955
Atomic solvation parameters applied to molecular dynamics of proteins in solutionQ24676145
The ultrahigh resolution crystal structure of ribonuclease A containing an isoaspartyl residue: hydration and sterochemical analysisQ27621833
High-resolution three-dimensional structure of ribonuclease A in solution by nuclear magnetic resonance spectroscopyQ27732016
All-atom empirical potential for molecular modeling and dynamics studies of proteinsQ27860468
Effective energy function for proteins in solutionQ28142746
Conformations of immunoglobulin hypervariable regionsQ28273335
Loops in globular proteins: a novel category of secondary structureQ28304573
A method for determining the positions of polar hydrogens added to a protein structure that maximizes protein hydrogen bondingQ30334411
Effects of temperature on protein structure and dynamics: X-ray crystallographic studies of the protein ribonuclease-A at nine different temperatures from 98 to 320 K.Q30343785
Taxonomy and conformational analysis of loops in proteins.Q30350131
Structure of antibody hypervariable loops reproduced by a conformational search algorithmQ30404853
Prediction of protein three-dimensional structures in insertion and deletion regions: a procedure for searching data bases of representative protein fragments using geometric scoring criteria.Q30416560
Comparison of systematic search and database methods for constructing segments of protein structureQ30418808
Free energy based populations of interconverting microstates of a cyclic peptide lead to the experimental NMR dataQ30579093
Modeling of globular proteins. A distance-based data search procedure for the construction of insertion/deletion regions and Pro----non-Pro mutationsQ34292073
Monte Carlo-minimization approach to the multiple-minima problem in protein foldingQ34347829
Conformational analysis and clustering of short and medium size loops connecting regular secondary structures: a database for modeling and predictionQ36279619
Free energy via molecular simulation: applications to chemical and biomolecular systemsQ38648060
Computer simulation of the free energy of peptides with the local states method: analogues of gonadotropin releasing hormone in the random coil and stable statesQ40685170
Computing the structure of bound peptides. Application to antigen recognition by class I major histocompatibility complex receptorsQ42610228
Long loops in proteinsQ42639084
Modeling protein loops using a phi i + 1, psi i dimer databaseQ42844816
Flexibility and function in HIV-1 proteaseQ44801403
Structural evidence for induced fit as a mechanism for antibody-antigen recognitionQ45203554
An algorithm for determining the conformation of polypeptide segments in proteins by systematic searchQ45559122
Modeling the anti-CEA antibody combining site by homology and conformational searchQ46604797
Backbone and side chain dynamics of uncomplexed human adipocyte and muscle fatty acid-binding proteinsQ48020079
A global taxonomy of loops in globular proteins.Q48785741
New efficient statistical sequence-dependent structure prediction of short to medium-sized protein loops based on an exhaustive loop classification.Q52211558
PDB-based protein loop prediction: parameters for selection and methods for optimization.Q52267152
Development of an extended simulated annealing method: Application to the modeling of complementary determining regions of immunoglobulinsQ52430167
Flap opening in HIV-1 protease simulated by 'activated' molecular dynamics.Q53849991
An automated classification of the structure of protein loops.Q53972089
Evaluation of the conformational free energies of loops in proteins.Q54641591
A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic MoleculesQ55918670
Exploration of disorder in protein structures by X-ray restrained molecular dynamicsQ57000538
Polar hydrogen positions in proteins: Empirical energy placement and neutron diffraction comparisonQ57000556
An Efficient Mean Solvation Force Model for Use in Molecular Dynamics Simulations of Proteins in Aqueous SolutionQ57950560
Loop closure via bond scaling and relaxationQ58489338
Anti-insulin antibody structure and conformation. II. Molecular dynamics with explicit solventQ68181844
Predicting antibody hypervariable loop conformation. I. Ensembles of random conformations for ringlike structuresQ68557407
Predicting antibody hypervariable loop conformations. II: Minimization and molecular dynamics studies of MCPC603 from many randomly generated loop conformationsQ68704284
P433issue3
P407language of work or nameEnglishQ1860
P921main subjectprotein structureQ735188
P304page(s)303-314
P577publication date2001-05-01
P1433published inProteinsQ7251514
P1476titleOptimization of solvation models for predicting the structure of surface loops in proteins
P478volume43

Reverse relations

cites work (P2860)
Q33647707A novel Omp25-binding peptide screened by phage display can inhibit Brucella abortus 2308 infection in vitro and in vivo
Q42109476Development of a new physics-based internal coordinate mechanics force field and its application to protein loop modeling
Q30884801In vitro effect of a thrombin inhibition peptide selected by phage display technology.
Q41812957Minimalist explicit solvation models for surface loops in proteins
Q35933755Optimization of the GB/SA solvation model for predicting the structure of surface loops in proteins
Q37002751Prediction of protein loop structures using a local move Monte Carlo approach and a grid-based force field
Q40594020Solvation parameters for predicting the structure of surface loops in proteins: Transferability and entropic effects
Q37279410The effect of loops on the structural organization of alpha-helical membrane proteins
Q36838886Use of decoys to optimize an all-atom force field including hydration

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