US-align: universal structure alignments of proteins, nucleic acids, and macromolecular complexes

RNA-align: quick and accurate alignment of RNA 3D structures based on size-independent TM-scoreRNA

(2019) Sha Gong et al.   BIOINFORMATICS

RMalign: an RNA structural alignment tool based on a novel scoring function RMscore

(2019) Jinfang Zheng et al.   BMC GENOMICS

Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the Protein Data Bank (PDB)

(2019) Paul D. Adams et al.   Acta Crystallographica Section D-Structural Biology

Assembling multidomain protein structures through analogous global structural alignments

(2019) Xiaogen Zhou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

LS-align: an atom-level, flexible ligand structural alignment algorithm for high-throughput virtual screening

(2018) Jun Hu et al.   BIOINFORMATICS

MetaGO: Predicting Gene Ontology of Non-homologous Proteins Through Low-Resolution Protein Structure Prediction and Protein–Protein Network Mapping

(2018) Chengxin Zhang et al.   JOURNAL OF MOLECULAR BIOLOGY

TRRUST v2: an expanded reference database of human and mouse transcriptional regulatory interactions

(2017) Heonjong Han et al.   NUCLEIC ACIDS RESEARCH

COFACTOR: improved protein function prediction by combining structure, sequence and protein–protein interaction information

(2017) Chengxin Zhang et al.   NUCLEIC ACIDS RESEARCH

STRUM: structure-based prediction of protein stability changes upon single-point mutation

(2016) Lijun Quan et al.   BIOINFORMATICS

The coming of age of de novo protein design

(2016) Po-Ssu Huang et al.   NATURE

Topology independent comparison of RNA 3D structures using the CLICK algorithm

(2016) Minh N. Nguyen et al.   NUCLEIC ACIDS RESEARCH

Template-Based Modeling of Protein-RNA Interactions

(2016) Jinfang Zheng et al.   PLoS Computational Biology

MICAN : a protein structure alignment algorithm that can handle Multiple-chains, Inverse alignments, Cα only models, Alternative alignments, and Non-sequential alignments

(2013) Shintaro Minami et al.   BMC BIOINFORMATICS

SCOPe: Structural Classification of Proteins—extended, integrating SCOP and ASTRAL data and classification of new structures

(2013) Naomi K. Fox et al.   NUCLEIC ACIDS RESEARCH

An Evolution-Based Approach to De Novo Protein Design and Case Study on Mycobacterium tuberculosis

(2013) Pralay Mitra et al.   PLoS Computational Biology

How significant is a protein structure similarity with TM-score = 0.5?

(2010) Jinrui Xu et al.   BIOINFORMATICS

CD-HIT Suite: a web server for clustering and comparing biological sequences

(2010) Ying Huang et al.   BIOINFORMATICS

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

(2009) Srayanta Mukherjee et al.   NUCLEIC ACIDS RESEARCH

PROMALS3D: a tool for multiple protein sequence and structure alignments

(2008) Jimin Pei et al.   NUCLEIC ACIDS RESEARCH

Matt: Local Flexibility Aids Protein Multiple Structure Alignment

(2008) Matthew Menke et al.   PLoS Computational Biology