(Q30352261)

20 June 2017

title

Protein structure evaluation using an all-atom energy based empirical scoring function. (English)

1 reference

20 June 2017

Pooja Narang

1

1 reference

20 June 2017

Kukum Bhushan

series ordinal

2

1 reference

20 June 2017

Surojit Bose

series ordinal

3

1 reference

20 June 2017

B Jayaram

series ordinal

4

1 reference

20 June 2017

publication date

1 February 2006

1 reference

Journal of Biomolecular Structure and Dynamics

20 June 2017

published in

1 reference

20 June 2017

volume

23

1 reference

20 June 2017

issue

4

1 reference

20 June 2017

page(s)

385-406

1 reference

Free energy component analysis for drug design: a case study of HIV-1 protease-inhibitor binding

20 June 2017

cites work

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2006.10531234

A free energy based computational pathway from chemical templates to lead compounds: a case study of COX-2 inhibitors

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2006.10531234

Viewing protein folding from many perspectives

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2006.10531234

From folding theories to folding proteins: a review and assessment of simulation studies of protein folding and unfolding

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2006.10531234

Protein folding mechanisms: new methods and emerging ideas

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2006.10531234

All-atom simulations of protein folding and unfolding

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2006.10531234

From Levinthal to pathways to funnels

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2006.10531234

Folding proteins with a simple energy function and extensive conformational searching

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2006.10531234

Tertiary structure predictions on a comprehensive benchmark of medium to large size proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2006.10531234

Automated structure prediction of weakly homologous proteins on a genomic scale

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2006.10531234

Computer modeling of protein folding: conformational and energetic analysis of reduced and detailed protein models

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2006.10531234

Complete protein structure determination using backbone residual dipolar couplings and sidechain rotamer prediction.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2006.10531234

Computational studies of protein folding

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2006.10531234

Ab initio protein structure prediction.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2006.10531234

Protein folding: from the levinthal paradox to structure prediction

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2006.10531234

Thermodynamics of protein folding: a microscopic view

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2006.10531234

Protein folding: the endgame

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2006.10531234

Predicting protein three-dimensional structure.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2006.10531234

Ab initio protein folding.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2006.10531234

Protein folding: progress made and promises ahead

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2006.10531234

Ab initio protein folding using LINUS.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2006.10531234

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2006.10531234

A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2006.10531234

CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2006.10531234

Comparison of database potentials and molecular mechanics force fields

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2006.10531234

Empirical force fields for biological macromolecules: overview and issues.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2006.10531234

Improved treatment of the protein backbone in empirical force fields.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2006.10531234

Are database-derived potentials valid for scoring both forward and inverted protein folding?

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2006.10531234

Folding Lennard-Jones proteins by a contact potential.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2006.10531234

Knowledge-based potentials for protein folding: what can we learn from known protein structures?

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2006.10531234

Empirical potentials and functions for protein folding and binding.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2006.10531234

Native atom types for knowledge-based potentials: application to binding energy prediction.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2006.10531234

Analysis of knowledge-based protein-ligand potentials using a self-consistent method

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2006.10531234

Effective energy functions for protein structure prediction.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2006.10531234

Knowledge-based potentials for proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2006.10531234

A distance-dependent atomic knowledge-based potential for improved protein structure selection.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2006.10531234

Structure-derived potentials and protein simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2006.10531234

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2006.10531234

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2006.10531234

Discrimination of native protein structures using atom-atom contact scoring

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2006.10531234

Ab initio fold prediction of small helical proteins using distance geometry and knowledge-based scoring functions

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2006.10531234

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2006.10531234

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2006.10531234

Free-energy calculations highlight differences in accuracy between X-ray and NMR structures and add value to protein structure prediction.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2006.10531234

Identifying native-like protein structures using physics-based potentials

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2006.10531234

How well can we predict native contacts in proteins based on decoy structures and their energies?

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2006.10531234

An improved protein decoy set for testing energy functions for protein structure prediction.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2006.10531234

Distinguish protein decoys by using a scoring function based on a new AMBER force field, short molecular dynamics simulations, and the generalized born solvent model

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2006.10531234

Physical scoring function based on AMBER force field and Poisson-Boltzmann implicit solvent for protein structure prediction.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2006.10531234

Energetic coupling between DNA bending and base pair opening

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2006.10531234

Comparison of simple potential functions for simulating liquid water

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2006.10531234

Contributions of the thymine methyl group to the specific recognition of poly- and mononucleotides: an analysis of the relative free energies of solvation of thymine and uracil.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2006.10531234

SWISS-MODEL: An automated protein homology-modeling server

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2006.10531234

SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2006.10531234

ESyPred3D: Prediction of proteins 3D structures.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2006.10531234

Enhancement of protein modeling by human intervention in applying the automatic programs 3D-JIGSAW and 3D-PSSM.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2006.10531234

A computational pathway for bracketing native-like structures fo small alpha helical globular proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2006.10531234

Evaluation of protein models by atomic solvation preference.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2006.10531234

Ab initio construction of protein tertiary structures using a hierarchical approach

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2006.10531234

A Novel Approach to Decoy Set Generation: Designing a Physical Energy Function Having Local Minima with Native Structure Characteristics

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2006.10531234

Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2006.10531234

A comprehensive analysis of 40 blind protein structure predictions

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2006.10531234

Consensus structural models for the amino terminal domain of the retrovirus restriction gene Fv1 and the murine leukaemia virus capsid proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2006.10531234

Protein Modeling by E-mail

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2006.10531234

Distinguishing native conformations of proteins from decoys with an effective free energy estimator based on the OPLS all-atom force field and the Surface Generalized Born solvent model

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2006.10531234

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2006.10531234

Development of Physics-Based Energy Functions that Predict Medium-Resolution Structures for Proteins of the α, β, and α/β Structural Classes

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2006.10531234

10.1080/07391102.2006.10531234

21 January 2018

Identifiers

DOI

1 reference

20 June 2017

1 reference