GRAFENE: Graphlet-based alignment-free network approach integrates 3D structural and sequence (residue order) data to improve protein structural comparison

Exploring the structure and function of temporal networks with dynamic graphlets

(2015) Y. Hulovatyy et al.   BIOINFORMATICS

Proper evaluation of alignment-free network comparison methods

(2015) Ömer Nebil Yaveroğlu et al.   BIOINFORMATICS

Dynamic networks reveal key players in aging

(2014) Fazle E. Faisal et al.   BIOINFORMATICS

GR-Align: fast and flexible alignment of protein 3D structures using graphlet degree similarity

(2014) Noël Malod-Dognin et al.   BIOINFORMATICS

Expanding Anfinsen’s Principle: Contributions of Synonymous Codon Selection to Rational Protein Design

(2014) Ian M. Sander et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Gene Ontology Consortium: going forward

(2014)   NUCLEIC ACIDS RESEARCH

CATH: comprehensive structural and functional annotations for genome sequences

(2014) Ian Sillitoe et al.   NUCLEIC ACIDS RESEARCH

Revealing Missing Parts of the Interactome via Link Prediction

(2014) Yuriy Hulovatyy et al.   PLoS One

A novel method for similarity/dissimilarity analysis of protein sequences

(2013) Zengchao Mu et al.   PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS

Graphlet-based edge clustering reveals pathogen-interacting proteins

(2012) R. W. Solava et al.   BIOINFORMATICS

An α Helix to β Barrel Domain Switch Transforms the Transcription Factor RfaH into a Translation Factor

(2012) Björn M. Burmann et al.   CELL

Residue centrality in alpha helical polytopic transmembrane protein structures

(2012) I. Arnold Emerson et al.   JOURNAL OF THEORETICAL BIOLOGY

Maximum Contact Map Overlap Revisited

(2011) Rumen Andonov et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Network analysis of transmembrane protein structures

(2011) I. Arnold Emerson et al.   PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS

Dominating Biological Networks

(2011) Tijana Milenković et al.   PLoS One

Dali server: conservation mapping in 3D

(2010) Liisa Holm et al.   NUCLEIC ACIDS RESEARCH

Advances and pitfalls of protein structural alignment

(2009) Hitomi Hasegawa et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Optimized Null Model for Protein Structure Networks

(2009) Tijana Milenković et al.   PLoS One

Conserved network properties of helical membrane protein structures and its implication for improving membrane protein homology modeling at the twilight zone

(2008) Jun Gao et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Rare Codons Cluster

(2008) Thomas F. Clarke et al.   PLoS One

Interconversion between two unrelated protein folds in the lymphotactin native state

(2008) Robbyn L. Tuinstra et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Network pattern of residue packing in helical membrane proteins and its application in membrane protein structure prediction

(2008) Vagmita Pabuwal et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Comparative analysis of the packing topology of structurally important residues in helical membrane and soluble proteins

(2008) Vagmita Pabuwal et al.   PROTEIN ENGINEERING DESIGN & SELECTION

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

(2007) Mickey Kosloff et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS