(Q30329417)

1 September 2017

Statistical potentials for fold assessment. (English)

1 reference

1 September 2017

0 references

3

Andrej Sali

0 references

author name string

Francisco Melo

series ordinal

1

1 reference

PMC publication ID

2373452

1 September 2017

Roberto Sánchez

series ordinal

2

1 reference

1 September 2017

1 February 2002

1 reference

1 September 2017

1 reference

1 September 2017

11

1 reference

1 September 2017

2

1 reference

1 September 2017

430-448

1 reference

Stereochemistry of polypeptide chain configurations

1 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373452

Implicit Solvation Models: Equilibria, Structure, Spectra, and Dynamics

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373452

Protein structure prediction and structural genomics

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373452

Ab initio protein structure prediction: progress and prospects.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373452

Recent improvements in prediction of protein structure by global optimization of a potential energy function.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373452

Free energy determinants of tertiary structure and the evaluation of protein models.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373452

Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373452

Discrimination of near-native protein structures from misfolded models by empirical free energy functions.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373452

Modeling of loops 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=2373452

How to generate improved potentials for protein tertiary structure prediction: a lattice model study.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373452

Comparative protein structure modeling of genes and genomes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373452

Ab initio construction of protein tertiary structures using a hierarchical 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=2373452

Use of MM-PB/SA in estimating the free energies of proteins: application to native, intermediates, and unfolded villin headpiece

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373452

Effective energy functions for protein structure 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=2373452

3 June 2018

The Protein Data Bank

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373452

Ab initio folding of proteins using restraints derived from evolutionary information

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373452

Protein secondary structure prediction based on position-specific scoring matrices

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373452

Knowledge-based interaction potentials for 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=2373452

Discrimination of the native from misfolded protein models with an energy function including implicit solvation

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373452

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373452

Pair potentials for protein folding: choice of reference states and sensitivity of predicted native states to variations in the interaction schemes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373452

Solution conformations and thermodynamics of structured peptides: molecular dynamics simulation with an implicit solvation model.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373452

Large-scale protein structure modeling of the Saccharomyces cerevisiae genome

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373452

Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit solvent continuum model

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373452

Generalized affine gap costs for protein sequence alignment

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373452

Different derivations of knowledge‐based potentials and analysis of their robustness and context‐dependent predictive power

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373452

Influence of protein structure databases on the predictive power of statistical pair potentials

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373452

Assessing protein structures with a non-local atomic interaction energy.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373452

An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction 1 1Edited by F. Cohen

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373452

Residue-residue mean-force potentials for protein structure recognition.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373452

CATH--a hierarchic classification of protein domain 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=2373452

Contact area difference (CAD): a robust measure to evaluate accuracy of protein models

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373452

Comparison of database potentials and molecular mechanics force fields

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373452

Empirical potentials and functions for protein folding and binding.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373452

Perspectives in protein-fold recognition

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373452

Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373452

Occluded molecular surface: analysis of protein packing

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373452

Deviations from standard atomic volumes as a quality measure for protein crystal 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=2373452

Are database-derived potentials valid for scoring both forward and inverted protein 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=2373452

Potential energy functions for threading

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373452

Structure-derived potentials and protein simulations

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373452

Protein structure prediction by threading methods: evaluation of current 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=2373452

Energy functions that discriminate X-ray and near native folds from well-constructed decoys

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373452

An empirical energy function for threading protein sequence through the folding motif

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373452

Reduced representation model of protein structure prediction: statistical potential and genetic algorithms

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373452

Verification of protein structures: patterns of nonbonded atomic interactions

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373452

Prediction of protein structure by evaluation of sequence-structure fitness. Aligning sequences to contact profiles derived from three-dimensional 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=2373452

Boltzmann's principle, knowledge-based mean fields and protein folding. An approach to the computational determination of 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=2373452

An improved pair potential to recognize native protein folds

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373452

An evolutionary approach to folding small alpha-helical proteins that uses sequence information and an empirical guiding fitness function

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373452

Comparative modelling of major house dust mite allergen Der p I: structure validation using an extended environmental amino acid propensity table

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373452

Knowledge-based potentials for 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=2373452

An analysis of incorrectly folded protein models. Implications for structure predictions.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373452

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=2373452

Solvation energy in protein folding and binding

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373452

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=2373452

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=2373452

Protein model structure evaluation using the solvation free energy 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=2373452

WHAT IF: a molecular modeling and drug design program

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373452

Protein folding. Effect of packing density on chain conformation

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373452

A Method to Identify Protein Sequences That Fold into a Known Three-Dimensional 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=2373452

Empirical solvation models can be used to differentiate native from near-native conformations of bovine pancreatic trypsin inhibitor

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373452

A new approach to protein fold recognition

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373452

Detection of native-like models for amino acid sequences of unknown three-dimensional structure in a data base of known protein 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=2373452

Evaluation of protein models by atomic solvation preference.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373452

Stereochemical quality of protein structure coordinates

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373452

Structure-derived hydrophobic potential. Hydrophobic potential derived from X-ray structures of globular proteins is able to identify native folds

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373452

Assessment of protein models with three-dimensional profiles

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373452

Topology fingerprint approach to the inverse protein folding problem

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373452

Contact potential that recognizes the correct folding of 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=2373452

Reductive Amination of Aldehydes and Ketones with Sodium Triacetoxyborohydride. Studies on Direct and Indirect Reductive Amination Procedures(1).

3 June 2018

1 reference

Molecular basis of HIV-1 protease drug resistance: structural analysis of mutant proteases complexed with cyclic urea inhibitors

21 January 2018

1 reference

Counteracting HIV-1 protease drug resistance: structural analysis of mutant proteases complexed with XV638 and SD146, cyclic urea amides with broad specificities

21 January 2018

1 reference

Structural basis of drug resistance for the V82A mutant of HIV-1 proteinase

21 January 2018

1 reference

Three-dimensional Structure of a Mutant HIV-1 Protease Displaying Cross-resistance to All Protease Inhibitors in Clinical Trials

21 January 2018

1 reference

Construction and use of lambda PL promoter vectors for direct cloning and high level expression of PCR amplified DNA coding sequences

21 January 2018

1 reference

In vivo emergence of HIV-1 variants resistant to multiple protease inhibitors

21 January 2018

1 reference

The HIV-1 protease as a therapeutic target for AIDS

21 January 2018

1 reference

Kinetic Properties of Saquinavir-Resistant Mutants of Human Immunodeficiency Virus Type 1 Protease and Their Implications in Drug Resistance in Vivo

21 January 2018

1 reference

Kinetic characterization and cross-resistance patterns of HIV-1 protease mutants selected under drug pressure

21 January 2018

1 reference

Crystal structures of complexes of a peptidic inhibitor with wild-type and two mutant HIV-1 proteases

21 January 2018

1 reference

Structure of a G48H mutant of HIV‐1 protease explains how glycine‐48 replacements produce mutants resistant to inhibitor drugs1

21 January 2018

1 reference

Active‐site mobility in human immunodeficiency virus, type 1, protease as demonstrated by crystal structure of A28S mutant

21 January 2018

1 reference

Errors in protein structures

21 January 2018

1 reference

Large scale purification and refolding of HIV-1 protease from Escherichia coli inclusion bodies.

21 January 2018

1 reference

Resistance to HIV Protease Inhibitors: A Comparison of Enzyme Inhibition and Antiviral Potency

21 January 2018

1 reference

PROCHECK: a program to check the stereochemical quality of protein structures

21 January 2018

1 reference

Effect of point mutations on the kinetics and the inhibition of human immunodeficiency virus type 1 protease: relationship to drug resistance

21 January 2018

1 reference

Peptide substrates and inhibitors of the HIV-1 protease

21 January 2018

1 reference

Non-active site changes elicit broad-based cross-resistance of the HIV-1 protease to inhibitors

21 January 2018

1 reference

Kinetic characterization of human immunodeficiency virus type-1 protease-resistant variants

21 January 2018

1 reference

Domain Flexibility in Retroviral Proteases: Structural Implications for Drug Resistant Mutations,

21 January 2018

1 reference

Mutational anatomy of an HIV-1 protease variant conferring cross-resistance to protease inhibitors in clinical trials. Compensatory modulations of binding and activity

21 January 2018

1 reference

Inhibition and catalytic mechanism of HIV-1 aspartic protease

21 January 2018

1 reference

Structural role of the 30's loop in determining the ligand specificity of the human immunodeficiency virus protease

21 January 2018

1 reference

Structural biology of HIV.

21 January 2018

1 reference

Escape mutants of HIV-1 proteinase: enzymic efficiency and susceptibility to inhibition

21 January 2018

1 reference

Structure-based inhibitors of HIV-1 protease

21 January 2018

1 reference

Structural and biochemical studies of retroviral proteases

21 January 2018

1 reference

MODBASE, a database of annotated comparative protein structure models.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373452

Identification and ab initio simulations of early folding units in 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=2373452

Free energy calculations on dimer stability of the HIV protease using molecular dynamics and a continuum solvent model

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373452

Comparison of two optimization methods to derive energy parameters for protein folding: perceptron and Z score

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373452

Identifying sequence-structure pairs undetected by sequence alignments

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373452

On the design and analysis of protein folding potentials

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373452

Combination of threading potentials and sequence profiles improves fold recognition.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373452

Can a pairwise contact potential stabilize native protein folds against decoys obtained by threading?

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373452

A method for the improvement of threading-based protein models

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373452

A computational approach to simplifying the protein folding alphabet

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373452

Validation of protein models derived from experiment

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373452

Successful ab initio prediction of the tertiary structure of NK‐lysin using multiple sequences and recognized supersecondary structural motifs

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373452

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=2373452

Stability changes upon mutation of solvent-accessible residues in proteins evaluated by database-derived potentials

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373452

Statistical potentials extracted from protein structures: how accurate are they?

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373452

Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373452

Factors influencing the ability of knowledge-based potentials to identify native sequence-structure matches

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373452

Derivation of protein-specific pair potentials based on weak sequence fragment similarity

26 November 2018

1 reference

12 December 2020

Criteria that discriminate between native proteins and incorrectly folded models

1 reference

12 December 2020

Predicting protein stability changes upon mutation using database-derived potentials: solvent accessibility determines the importance of local versus non-local interactions along the sequence

1 reference

12 December 2020

The frequency of ion-pair substructures in proteins is quantitatively related to electrostatic potential: a statistical model for nonbonded interactions

1 reference

12 December 2020

Evaluation of atomic level mean force potentials via inverse folding and inverse refinement of protein structures: atomic burial position and pairwise non-bonded interactions

1 reference

12 December 2020

Factors affecting the ability of energy functions to discriminate correct from incorrect folds

1 reference

12 December 2020

Polar and nonpolar atomic environments in the protein core: implications for folding and binding

1 reference

12 December 2020

Correctly folded proteins make twice as many hydrophobic contacts

1 reference

12 December 2020

Identification of native protein folds amongst a large number of incorrect models. The calculation of low energy conformations from potentials of mean force

1 reference

12 December 2020

Tertiary structure prediction using mean-force potentials and internal energy functions: successful prediction for coiled-coil geometries

1 reference

12 December 2020

Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins

1 reference

12 December 2020

Distance-dependent, pair potential for protein folding: results from linear optimization

1 reference

12 December 2020

Recognizing native folds by the arrangement of hydrophobic and polar residues

1 reference

12 December 2020

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

1 reference

12 December 2020

Polarity as a criterion in protein design

1 reference

12 December 2020

Identifiers

DOI

10.1110/PS.25502

1 reference

1 September 2017

1 reference

PMC publication ID

2373452

1 September 2017

PubMed publication ID

11790853

1 reference

PMC publication ID

2373452