ORIGINAL PAPER A user-friendly web portal for analyzing conformational changes in structures of Mycobacterium tuberculosis Sameer Hassan 1 & Manonanthini Thangam 1 & Praveen Vasudevan 1 & G. Ramesh Kumar 2 & Rahul Unni 1 & P. K. Gayathri Devi 1 & Luke Elizabeth Hanna 1,3 Received: 26 February 2015 /Accepted: 24 August 2015 # Springer-Verlag Berlin Heidelberg 2015 Abstract Initiation of the Tuberculosis Structural Consor- tium has resulted in the expansion of the Mycobacterium tu- berculosis (MTB) protein structural database. Currently, 969 experimentally solved structures are available for 354 MTB proteins. This includes multiple crystal structures for a given protein under different functional conditions, such as the presence of different ligands or mutations. In depth anal- ysis of the multiple structures reveal that subtle differences exist in conformations of a given protein under varied conditions. Therefore, it is immensely important to under- stand the conformational differences between the multiple structures of a given protein in order to select the most suitable structure for molecular docking and structure- based drug designing. Here, we introduce a web portal (http://bmi.icmr.org.in/mtbsd/torsion.php) that we developed to provide comparative data on the ensemble of available structures of MTB proteins, such as Cα root means square deviation (RMSD), sequence identity, presence of mutations and torsion angles. Additionally, torsion angles were used to perform principal component analysis (PCA) to identify the conformational differences between the structures. Additionally, we present a few case studies to demonstrate this database. Keywords Principal component analysis . Proteins . RMSD . Structures . Torsion angles Introduction Tuberculosis (TB) was declared a global health emergency in 1993. The World Health Organisation estimated 8.7 million new cases of TB and 1.4 million TB-related deaths worldwide in 2011 [1]. The whole genome of Mycobacterium tuberculo- sis (4.4 MB), the etiological agent of TB, was first sequenced in 1998 [2] and it is reported to contain 4018 protein coding genes. More than half of the MTB genome still remains uncharacterized (hypothetical proteins), thus limiting our un- derstanding on its pathogenicity and hindering the search for new drug targets [3]. Structural bioinformatics is a comple- mentary method used for annotating protein sequences having undetectable homologous sequences in databases and also for studying the conformational changes that occur upon binding to ligands. There are 969 structures currently available for 354 unique proteins of MTB in the Mycobacterium tuberculosis Structural Database (MtbSD) [4], implying that there are mul- tiple structures for many of these proteins. Structural studies comparing holo and apo forms of pro- teins have shown that binding of ligand is often coupled with a conformational change in the interacting partners [5–7]. There are 42 MTB genes listed in MtbSD that have structures both in apo and holo forms. For example, inhA gene of MTB has 32 solved structures that include wild type, mutant, apo,and holo forms of the protein in complex with different ligands. A comparative analysis of the various structures of a given pro- tein will help us understand the extent of alteration in protein Electronic supplementary material The online version of this article (doi:10.1007/s00894-015-2799-6) contains supplementary material, which is available to authorized users. * Luke Elizabeth Hanna hannatrc@yahoo.com 1 Department of Biomedical Informatics, National Institute for Research in Tuberculosis, Chetpet, Chennai 600 031, India 2 AU-KBC Research Centre, Madras Institute of Technology, Anna University, Chromepet, Chennai, India 3 Department of Clinical Research, National Institute for Research in Tuberculosis, Chetpet, Chennai 600 031, India J Mol Model (2015) 21:252 DOI 10.1007/s00894-015-2799-6