Modeling of loops in protein structures (Q29615861)

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=11045621

30 April 2017

author name string

Fiser A

series ordinal

1

1 reference

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30 April 2017

Do RK

series ordinal

2

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=11045621

30 April 2017

Sali A

series ordinal

3

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=11045621

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=11045621

30 April 2017

language of work or name

1 reference

30 April 2017

publication date

September 2000

1 reference

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30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=11045621

30 April 2017

volume

9

1 reference

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30 April 2017

issue

9

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=11045621

30 April 2017

page(s)

1753-73

1 reference

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30 April 2017

1 reference

https://salilab.org/modeller/

Stereochemistry of polypeptide chain configurations

21 September 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

Comparative protein structure modeling of genes and genomes

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

Large-scale protein structure modeling of the Saccharomyces cerevisiae genome

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

Fold and function predictions for Mycoplasma genitalium proteins

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

Crystal structure of the delta' subunit of the clamp-loader complex of E. coli DNA polymerase III

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

Protein engineering with monomeric triosephosphate isomerase (monoTIM): the modelling and structure verification of a seven-residue loop

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

Ligand specificity of brain lipid-binding protein

30 April 2017

1 reference

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Comparative protein modelling by satisfaction of spatial restraints

30 April 2017

1 reference

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Recognition of errors in three-dimensional structures of proteins

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

Structural basis of substrate specificity in the serine proteases

30 April 2017

1 reference

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Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

Conformations of immunoglobulin hypervariable regions

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

Conformation of beta-hairpins in protein structures. A systematic classification with applications to modelling by homology, electron density fitting and protein engineering

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

Database of homology-derived protein structures and the structural meaning of sequence alignment

30 April 2017

1 reference

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Accurate modeling of protein conformation by automatic segment matching

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

Assessment of protein models with three-dimensional profiles

30 April 2017

1 reference

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ModBase: a database of comparative protein structure models.

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

CASP3 comparative modeling evaluation

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

Critical assessment of methods of protein structure prediction (CASP): round III.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

Are predicted structures good enough to preserve functional sites?

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

Flexible ligand docking: a multistep strategy approach

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

Prediction of the location and type of beta-turns in proteins using neural networks.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

Protein-DNA interactions: A structural analysis

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

Structural motif of phosphate-binding site common to various protein superfamilies: all-against-all structural comparison of protein-mononucleotide complexes

3 June 2018

1 reference

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Three-dimensional structure analysis of PROSITE patterns

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

Recognition of spatial motifs in protein structures

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

Supersites within superfolds. Binding site similarity in the absence of homology

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

Functional analysis of the Escherichia coli genome using the sequence-to-structure-to-function paradigm: identification of proteins exhibiting the glutaredoxin/thioredoxin disulfide oxidoreductase activity.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

Homology-based fold predictions for Mycoplasma genitalium proteins

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

A graph-theoretic algorithm for comparative modeling of protein structure

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

Evaluation of comparative protein structure modeling by MODELLER-3.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

Does conformational free energy distinguish loop conformations in proteins?

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

Engineering metal-binding sites in proteins

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

Structure-based design and combinatorial chemistry yield low nanomolar inhibitors of cathepsin D.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

PDB-based protein loop prediction: parameters for selection and methods for optimization.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

Predicting the conformational class of short and medium size loops connecting regular secondary structures: application to comparative modelling

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

Advances in comparative protein-structure modelling

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

Conformational analysis and clustering of short and medium size loops connecting regular secondary structures: a database for modeling and prediction

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

Structural families in loops of homologous proteins: automatic classification, modelling and application to antibodies

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

A structural explanation for the twilight zone of protein sequence homology

3 June 2018

1 reference

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Accuracy and reliability of the scaling-relaxation method for loop closure: an evaluation based on extensive and multiple copy conformational samplings

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

Functional significance of loops in the receptor binding domain of Bacillus thuringiensis CryIIIA delta-endotoxin

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

Automatic classification and analysis of alpha alpha-turn motifs in proteins

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

Structure-based inhibitor design by using protein models for the development of antiparasitic agents

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

Fragment ranking in modelling of protein structure. Conformationally constrained environmental amino acid substitution tables.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

Modeling of protein loops by simulated annealing

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

Determining protein loop conformation using scaling-relaxation techniques

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

Origins of structural diversity within sequentially identical hexapeptides

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

Comparison of conformational characteristics in structurally similar protein pairs

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

Computing the structure of bound peptides. Application to antigen recognition by class I major histocompatibility complex receptors

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

Evaluation of the conformational free energies of loops in proteins.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

Multiple copy sampling in protein loop modeling: computational efficiency and sensitivity to dihedral angle perturbations

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

Comparison of systematic search and database methods for constructing segments of protein structure

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

Modeling protein loops using a ϕi+1, Ψi dimer database

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

Enhanced conformational sampling in Monte Carlo simulations of proteins: application to a constrained peptide

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

De novo prediction of polypeptide conformations using dihedral probability grid Monte Carlo methodology

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

Simultaneous modeling of multiple loops in proteins

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

A self consistent mean field approach to simultaneous gap closure and side-chain positioning in homology modelling

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

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.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

Model for haptoglobin heavy chain based upon structural homology

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

The consistency principle in protein structure and pathways of folding

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

A possible three-dimensional structure of bovine α-lactalbumin based on that of hen's egg-white lysozyme

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

Mapping protein dynamics by X-ray diffraction

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

Using known substructures in protein model building and crystallography

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

Knowledge-based prediction of protein structures and the design of novel molecules

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

Structure of antibody hypervariable loops reproduced by a conformational search algorithm

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

An algorithm for determining the conformation of polypeptide segments in proteins by systematic search

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

Modelling the polypeptide backbone with 'spare parts' from known protein structures

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

Structural determinants of the conformations of medium-sized loops in proteins

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

Modeling antibody hypervariable loops: a combined algorithm.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

Modeling of globular proteins. A distance-based data search procedure for the construction of insertion/deletion regions and Pro----non-Pro mutations

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

Determining minimum energy conformations of polypeptides by dynamic programming

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

Development of an extended simulated annealing method: Application to the modeling of complementary determining regions of immunoglobulins

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

Common features of the conformations of antigen-binding loops in immunoglobulins and application to modeling loop conformations

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

Taxonomy and conformational analysis of loops in proteins.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

Modeling the anti-CEA antibody combining site by homology and conformational search

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

Search for the stable state of a short chain in a molecular field

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

A novel exhaustive search algorithm for predicting the conformation of polypeptide segments in proteins.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

Free energy landscapes of peptides by enhanced conformational sampling.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

New efficient statistical sequence-dependent structure prediction of short to medium-sized protein loops based on an exhaustive loop classification.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

ABGEN: a knowledge-based automated approach for antibody structure modeling

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

Assessment of comparative modeling in CASP2.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

Prediction of protein-protein interaction sites using patch analysis

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

An automated classification of the structure of protein loops.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

Novel knowledge-based mean force potential at atomic level

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

The main-chain dynamics of the dynamin pleckstrin homology (PH) domain in solution: analysis of 15N relaxation with monomer/dimer equilibration 1 1 Edited by P.E.Wright

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

A global taxonomy of loops in globular proteins.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

Exhaustive conformational search and simulated annealing for models of lattice peptides.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

Empirical and structural models for insertions and deletions in the divergent evolution of proteins.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

Predicting immunoglobulin-like hypervariable loops.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

The loop problem in proteins: A monte carlo simulated annealing approach

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

Prediction of hypervariable CDR-H3 loop structures in antibodies.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

Multiple copy sampling: rigid versus flexible protein.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144714

100,000 protein structures for the biologist

26 November 2018

1 reference

https://pubmed.ncbi.nlm.nih.gov/11045621

12 December 2020

Prediction of loop geometries using a generalized born model of solvation effects

1 reference

https://pubmed.ncbi.nlm.nih.gov/11045621

12 December 2020

Improvement of turn structure prediction by molecular dynamics: a case study of alpha 1-purothionin

1 reference

https://pubmed.ncbi.nlm.nih.gov/11045621

12 December 2020

Anti-insulin antibody structure and conformation. II. Molecular dynamics with explicit solvent

1 reference

https://pubmed.ncbi.nlm.nih.gov/11045621

12 December 2020

Analysis of two-residue turns in proteins

1 reference

https://pubmed.ncbi.nlm.nih.gov/11045621

12 December 2020

1 reference

https://pubmed.ncbi.nlm.nih.gov/11045621

12 December 2020

Molecular dynamics of native protein. II. Analysis and nature of motion

1 reference

https://pubmed.ncbi.nlm.nih.gov/11045621

12 December 2020

Turn prediction in proteins using a pattern-matching approach

1 reference

https://pubmed.ncbi.nlm.nih.gov/11045621

12 December 2020

The predicted structure of immunoglobulin D1.3 and its comparison with the crystal structure

1 reference

https://pubmed.ncbi.nlm.nih.gov/11045621

12 December 2020

Prediction of the folding of short polypeptide segments by uniform conformational sampling

1 reference

https://pubmed.ncbi.nlm.nih.gov/11045621

12 December 2020

Canonical structures for the hypervariable regions of immunoglobulins

1 reference

https://pubmed.ncbi.nlm.nih.gov/11045621

12 December 2020

Predicting antibody hypervariable loop conformation. I. Ensembles of random conformations for ringlike structures

1 reference

https://pubmed.ncbi.nlm.nih.gov/11045621

12 December 2020

Predicting antibody hypervariable loop conformations. II: Minimization and molecular dynamics studies of MCPC603 from many randomly generated loop conformations

1 reference

https://pubmed.ncbi.nlm.nih.gov/11045621

12 December 2020

Conformational sampling using high-temperature molecular dynamics

1 reference

https://pubmed.ncbi.nlm.nih.gov/11045621

12 December 2020

Analysis of insertions/deletions in protein structures

1 reference

https://pubmed.ncbi.nlm.nih.gov/11045621

12 December 2020

A critical assessment of comparative molecular modeling of tertiary structures of proteins

1 reference

https://pubmed.ncbi.nlm.nih.gov/11045621

12 December 2020

Protein-protein interaction at crystal contacts

1 reference

https://pubmed.ncbi.nlm.nih.gov/11045621

12 December 2020

Comparison of an antibody model with an X-ray structure: the variable fragment of BR96

1 reference

https://pubmed.ncbi.nlm.nih.gov/11045621

12 December 2020

Homology modeling with internal coordinate mechanics: deformation zone mapping and improvements of models via conformational search

1 reference

https://pubmed.ncbi.nlm.nih.gov/11045621

12 December 2020

Chameleon sequences in the PDB

1 reference

https://pubmed.ncbi.nlm.nih.gov/11045621

12 December 2020

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=11045621

Identifiers

2 references

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=11045621

2 references

30 April 2017

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=11045621

PubMed publication ID

2 references

30 April 2017