List of works - Rachel Kolodny

A Novel Geometry-Based Approach to Infer Protein Interface Similarity.

scientific article published on 29 May 2018

A library of protein surface patches discriminates between native structures and decoys generated by structure prediction servers ⬇️

scientific article published on May 4, 2011

Approximate protein structural alignment in polynomial time

scientific article

Bridging Themes: Short Protein Segments Found in Different Architectures

scientific article published on 01 May 2021

Complex evolutionary footprints revealed in an analysis of reused protein segments of diverse lengths

scientific article published on 19 October 2017

Comprehensive evaluation of protein structure alignment methods: scoring by geometric measures.

scientific article

ConTemplate Suggests Possible Alternative Conformations for a Query Protein of Known Structure

scientific article

CyToStruct: Augmenting the Network Visualization of Cytoscape with the Power of Molecular Viewers

scientific article published on 9 April 2015

Efflux Pumps Represent Possible Evolutionary Convergence onto the Beta Barrel Fold

Efflux Pumps Represent Possible Evolutionary Convergence onto the β-Barrel Fold

scholarly article by Meghan Whitney Franklin published in September 2018

Evidence for the emergence of β-trefoils by ‘Peptide Budding’ from an IgG-like β-sandwich

scientific article published on 14 February 2022

Evolutionary pathways of repeat protein topology in bacterial outer membrane proteins

scientific article published on 29 November 2018

Faster algorithms for optimal multiple sequence alignment based on pairwise comparisons

scientific article published in October 2006

FragBag, an accurate representation of protein structure, retrieves structural neighbors from the entire PDB quickly and accurately.

scientific article

Global view of the protein universe

scientific article

In Silico Structural and Biochemical Functional Analysis of a Novel CYP21A2 Pathogenic Variant

scientific article published on 14 August 2020

Maps of protein structure space reveal a fundamental relationship between protein structure and function ⬇️

scientific article published on July 7, 2011

Navigating Among Known Structures in Protein Space

scientific article published on 01 January 2019

On the evolution of protein-adenine binding

scientific article published on 20 February 2020

On the universe of protein folds

scientific article

Protein structure comparison: implications for the nature of 'fold space', and structure and function prediction.

scientific article

Redundancy-weighting for better inference of protein structural features.

scientific article

Representation of the Protein Universe using Classifications, Maps, and Networks

Sequence-similar, structure-dissimilar protein pairs in the PDB.

scientific article

Similarity between the Usher Plug and the Repeating Domain of an Ice-adhesin: Evolution via Surface Reshaping

Small libraries of protein fragments model native protein structures accurately.

scientific article

Using ConTemplate and the PDB to explore conformational space: on the detection of rare protein conformations

scientific article

Using an alignment of fragment strings for comparing protein structures.

scientific article

VISTAL--a new 2D visualization tool of protein 3D structural alignments

scientific article published on 12 July 2006

List of works by Rachel Kolodny

A Novel Geometry-Based Approach to Infer Protein Interface Similarity.

A library of protein surface patches discriminates between native structures and decoys generated by structure prediction servers ⬇️

Approximate protein structural alignment in polynomial time

Bridging Themes: Short Protein Segments Found in Different Architectures

Complex evolutionary footprints revealed in an analysis of reused protein segments of diverse lengths

Comprehensive evaluation of protein structure alignment methods: scoring by geometric measures.

ConTemplate Suggests Possible Alternative Conformations for a Query Protein of Known Structure

CyToStruct: Augmenting the Network Visualization of Cytoscape with the Power of Molecular Viewers

Efflux Pumps Represent Possible Evolutionary Convergence onto the Beta Barrel Fold

Efflux Pumps Represent Possible Evolutionary Convergence onto the β-Barrel Fold

Evidence for the emergence of β-trefoils by ‘Peptide Budding’ from an IgG-like β-sandwich

Evolutionary pathways of repeat protein topology in bacterial outer membrane proteins

Faster algorithms for optimal multiple sequence alignment based on pairwise comparisons

FragBag, an accurate representation of protein structure, retrieves structural neighbors from the entire PDB quickly and accurately.

Global view of the protein universe

In Silico Structural and Biochemical Functional Analysis of a Novel CYP21A2 Pathogenic Variant

Maps of protein structure space reveal a fundamental relationship between protein structure and function ⬇️

Navigating Among Known Structures in Protein Space

On the evolution of protein-adenine binding

On the universe of protein folds

Protein structure comparison: implications for the nature of 'fold space', and structure and function prediction.

Redundancy-weighting for better inference of protein structural features.

Representation of the Protein Universe using Classifications, Maps, and Networks

Sequence-similar, structure-dissimilar protein pairs in the PDB.

Similarity between the Usher Plug and the Repeating Domain of an Ice-adhesin: Evolution via Surface Reshaping

Small libraries of protein fragments model native protein structures accurately.

Using ConTemplate and the PDB to explore conformational space: on the detection of rare protein conformations

Using an alignment of fragment strings for comparing protein structures.

VISTAL--a new 2D visualization tool of protein 3D structural alignments