(Q44706803)

5 December 2017

Simplicial neighborhood analysis of protein packing (SNAPP): a computational geometry approach to studying proteins (English)

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5 December 2017

computational biology

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inferred from title

computational geometry

1 reference

4

1 reference

5 December 2017

1

Alexander Tropsha

1 reference

5 December 2017

Charles W Carter

2

1 reference

PubMed ID

14696387

5 December 2017

Stephen Cammer

series ordinal

3

1 reference

PubMed ID

14696387

5 December 2017

language of work or name

English

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publication date

1 January 2003

1 reference

5 December 2017

Methods in Enzymology

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5 December 2017

374

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5 December 2017

509-544

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5 December 2017

The Protein Data Bank

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https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974022-1

7 January 2021

Blocks+: a non-redundant database of protein alignment blocks derived from multiple compilations.

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974022-1

7 January 2021

The PROSITE database, its status in 1999

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974022-1

7 January 2021

Touring protein fold space with Dali/FSSP

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974022-1

7 January 2021

Delaunay tessellation of proteins: four body nearest-neighbor propensities of amino acid residues

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974022-1

7 January 2021

Model of protein folding: inclusion of short-, medium-, and long-range interactions

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974022-1

7 January 2021

Computer simulation of protein folding

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974022-1

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974022-1

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974022-1

7 January 2021

Prediction of protein folding from amino acid sequence over discrete conformation spaces

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974022-1

7 January 2021

A new approach to protein fold recognition

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974022-1

7 January 2021

Pseudodihedrals: simplified protein backbone representation with knowledge-based energy

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974022-1

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974022-1

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974022-1

7 January 2021

Protein fold recognition and dynamics in the space of contact maps

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974022-1

7 January 2021

Folding proteins with a simple energy function and extensive conformational searching

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974022-1

7 January 2021

Knowledge-based potentials for proteins

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974022-1

7 January 2021

Potential energy functions for threading

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974022-1

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974022-1

7 January 2021

Contact potential that recognizes the correct folding of globular proteins

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974022-1

7 January 2021

Sequence-structure matching in globular proteins: application to supersecondary and tertiary structure determination

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974022-1

7 January 2021

Statistical significance of hierarchical multi-body potentials based on Delaunay tessellation and their application in sequence-structure alignment

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974022-1

7 January 2021

Development of a four-body statistical pseudo-potential to discriminate native from non-native protein conformations.

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974022-1

7 January 2021

A Geometrical Approach to the Structure Of Liquids

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974022-1

7 January 2021

The interpretation of protein structures: Total volume, group volume distributions and packing density

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974022-1

7 January 2021

Structural invariants in protein folding

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974022-1

7 January 2021

Volume occupation, environment and accessibility in proteins. The problem of the protein surface

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974022-1

7 January 2021

Calculation of protein volumes: an alternative to the Voronoi procedure

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974022-1

7 January 2021

Volume changes on protein folding.

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974022-1

7 January 2021

The packing density in proteins: standard radii and volumes.

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974022-1

7 January 2021

Calculations of protein volumes: sensitivity analysis and parameter database.

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974022-1

7 January 2021

Effective atom volumes for implicit solvent models: comparison between Voronoi volumes and minimum fluctuation volumes

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974022-1

7 January 2021

Voronoï tessellation reveals the condensed matter character of folded proteins

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974022-1

7 January 2021

Nonatomic solvent-driven Voronoi tessellation of proteins: an open tool to analyze protein folds.

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974022-1

7 January 2021

Quantification of protein surfaces, volumes and atom-atom contacts using a constrained Voronoi procedure.

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974022-1

7 January 2021

Lattice protein folding with two and four-body statistical potentials.

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974022-1

7 January 2021

Four-body potentials reveal protein-specific correlations to stability changes caused by hydrophobic core mutations.

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974022-1

7 January 2021

Analytical shape computation of macromolecules: I. Molecular area and volume through alpha shape.

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974022-1

7 January 2021

Analytical shape computation of macromolecules: II. Inaccessible cavities in proteins.

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974022-1

7 January 2021

Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974022-1

7 January 2021

Calculation of molecular volumes and areas for structures of known geometry.

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974022-1

7 January 2021

Water in protein cavities: A procedure to identify internal water and exchange pathways and application to fatty acid-binding protein

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974022-1

7 January 2021

A procedure for detection and quantitation of cavity volumes proteins. Application to measure the strength of the hydrophobic driving force in protein folding.

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974022-1

7 January 2021

A method to search for similar protein local structures at ligand binding sites and its application to adenine recognition

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974022-1

7 January 2021

Voronoi diagrams---a survey of a fundamental geometric data structure

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974022-1

7 January 2021

The interpretation of protein structures: Estimation of static accessibility

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974022-1

7 January 2021

Computing the n-dimensional Delaunay tessellation with application to Voronoi polytopes

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974022-1

7 January 2021

Enlarged representative set of protein structures

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974022-1

7 January 2021

Packing of alpha-helices onto beta-pleated sheets and the anatomy of alpha/beta proteins

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974022-1

7 January 2021

Structure of proteins: packing of alpha-helices and pleated sheets

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974022-1

7 January 2021

Helix to helix packing in proteins

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974022-1

7 January 2021

Determinants of strand register in antiparallel beta-sheets of proteins

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974022-1

7 January 2021

Selection of representative protein data sets

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974022-1

7 January 2021

Correctly folded proteins make twice as many hydrophobic contacts

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974022-1

7 January 2021

Correlation of sequence hydrophobicities measures similarity in three-dimensional protein structure

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974022-1

7 January 2021

Comparing the polarities of the amino acids: side-chain distribution coefficients between the vapor phase, cyclohexane, 1-octanol, and neutral aqueous solution

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974022-1

7 January 2021

Transition-state structure as a unifying basis in protein-folding mechanisms: contact order, chain topology, stability, and the extended nucleus mechanism

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974022-1

7 January 2021

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974022-1

7 January 2021

Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974022-1

7 January 2021

Patterned library analysis: a method for the quantitative assessment of hypotheses concerning the determinants of protein structure.

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974022-1

7 January 2021

10.1016/S0076-6879(03)74022-1

Identifiers

DOI

1 reference

5 December 2017

1 reference

PubMed ID

14696387