Finding optimal interaction interface alignments between biological complexes

How to find a leucine in a haystack? Structure, ligand recognition and regulation of leucine–aspartic acid (LD) motifs

(2014) Tanvir Alam et al.   BIOCHEMICAL JOURNAL

Modeling DNA affinity landscape through two-round support vector regression with weighted degree kernels

(2014) Xiaolei Wang et al.   BMC Systems Biology

Molecular evolution of protein-RNA mimicry as a mechanism for translational control

(2013) A. Katz et al.   NUCLEIC ACIDS RESEARCH

CoCiter: An Efficient Tool to Infer Gene Function by Assessing the Significance of Literature Co-Citation

(2013) Nan Qiao et al.   PLoS One

Accurate prediction of hot spot residues through physicochemical characteristics of amino acid sequences

(2013) Peng Chen et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

DNA hydrogel-based supercapacitors operating in physiological fluids

(2013) Jaehyun Hur et al.   Scientific Reports

A new size-independent score for pairwise protein structure alignment and its application to structure classification and nucleic-acid binding prediction

(2012) Yuedong Yang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Two small RNAs, CrcY and CrcZ, act in concert to sequester the Crc global regulator in Pseudomonas putida, modulating catabolite repression

(2011) Renata Moreno et al.   MOLECULAR MICROBIOLOGY

RNA mimicry, a decoy for regulatory proteins

(2011) S. Marzi et al.   MOLECULAR MICROBIOLOGY

iAlign: a method for the structural comparison of protein–protein interfaces

(2010) Mu Gao et al.   BIOINFORMATICS

Structure ofEscherichia coliAlkA in Complex with Undamaged DNA

(2010) Brian R. Bowman et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Structural Basis for NADH/NAD+ Redox Sensing by a Rex Family Repressor

(2010) Krystle J. McLaughlin et al.   MOLECULAR CELL

Structural Insight into the Sequence Dependence of Nucleosome Positioning

(2010) Bin Wu et al.   STRUCTURE

Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score

(2009) Shashi Pandit et al.   BMC BIOINFORMATICS

Advances and pitfalls of protein structural alignment

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

MM-align: a quick algorithm for aligning multiple-chain protein complex structures using iterative dynamic programming

(2009) Srayanta Mukherjee et al.   NUCLEIC ACIDS RESEARCH

Optimal contact map alignment of protein-protein interfaces

(2008) V. Pulim et al.   BIOINFORMATICS

Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments

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

Protein–protein interaction and quaternary structure

(2008) Joël Janin et al.   QUARTERLY REVIEWS OF BIOPHYSICS

Molecular mimicry: Structural camouflage of proteins and nucleic acids

(2007) Panagiotis A. Tsonis et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

MAMMOTH (Matching molecular models obtained from theory): An automated method for model comparison

(2002) Angel R. Ortiz et al.   PROTEIN SCIENCE