10.1186/1471-2105-6-240

Sequence variation in ligand binding sites in proteins
Cited by: 74
Author(s): Thomas J. Magliery, Lynne Regan
Software Mentions: 1
Published: almost 21 years ago

10.1186/1471-2105-12-264

MAVENs: Motion analysis and visualization of elastic networks and structural ensembles
Cited by: 37
Author(s): Michael T. Zimmermann, Andrzej Kloczkowski, Robert L. Jernigan
Software Mentions: 1
Published: about 15 years ago

10.1186/1471-2105-12-S1-S30

Hsp90/Cdc37 Chaperone/co-chaperone complex, a novel junction anticancer target elucidated by the mode of action of herbal drug Withaferin A
Cited by: 66
Author(s): Abhinav Grover, Ashutosh Shandilya, Vibhuti Agrawal, Piyush Pratik, Divya Bhasme, Virendra S. Bisaria, Durai Sundar
Software Mentions: 1
Published: over 15 years ago

10.1186/s12859-019-3254-y

HKPocket: human kinase pocket database for drug design
Cited by: 18
Author(s): Huiwen Wang, Jiadi Qiu, Haoquan Liu, Ying Xu, Ya Jia, Yunjie Zhao
Software Mentions: 1
Published: over 6 years ago

10.1186/1471-2105-10-S12-S15

Extraction, integration and analysis of alternative splicing and protein structure distributed information
Cited by: 0
Author(s): Matteo D’Antonio, Marco Masseroli
Software Mentions: 1
Published: almost 17 years ago

10.1186/1471-2105-10-207

Ensemble approach to predict specificity determinants: benchmarking and validation
Cited by: 24
Author(s): Saikat Chakrabarti, Anna R. Panchenko
Software Mentions: 1
Published: about 17 years ago

10.1186/1471-2105-12-414

Three-dimensional modeling of chromatin structure from interaction frequency data using Markov chain Monte Carlo sampling
Cited by: 158
Author(s): Mathieu Rousseau, James S. Fraser, Maria Ferraiuolo, Josée Dostie, Mathieu Blanchette
Software Mentions: 1
Published: almost 15 years ago

10.1186/s12859-017-1867-6

LCS-TA to identify similar fragments in RNA 3D structures
Cited by: 16
Author(s): Jakub Wiedemann, Tomasz Żok, Maciej Miłostan, Marta Szachniuk
Software Mentions: 1
Published: almost 9 years ago

10.1186/s12859-016-1339-4

Homology modeling and molecular dynamics provide structural insights into tospovirus nucleoprotein
Cited by: 10
Author(s): Rayane Nunes Lima, Muhammad Faheem, J.A.R.G. Barbosa, Marcelo Depólo Polêto, Hugo Verli, Fernando Lucas Melo, Renato O. Resende
Software Mentions: 1
Published: over 9 years ago

10.1186/1471-2105-10-S6-S13

A chemogenomics view on protein-ligand spaces
Cited by: 30
Author(s): Helena Strömbergsson, Gerard J. Kleywegt
Software Mentions: 1
Published: about 17 years ago

10.1186/1471-2105-15-196

Structure- and context-based analysis of the GxGYxYP family reveals a new putative class of Glycoside Hydrolase
Cited by: 8
Author(s): Daniel J. Rigden, Ruth Y Eberhardt, Harry J. Gilbert, Qingping Xu, Yuanyuan Chang, Adam Godzik
Software Mentions: 1
Published: about 12 years ago

10.1186/s12859-014-0416-9

Unique features of apicoplast DNA gyrases from Toxoplasma gondii and Plasmodium falciparum
Cited by: 14
Author(s): Soshichiro Nagano, Ting‐Yu Lin, Jyotheeswara R. Edula, Jonathan G. Heddle
Software Mentions: 1
Published: over 11 years ago

10.1186/s12859-014-0427-6

WEBnm@ v2.0: Web server and services for comparing protein flexibility
Cited by: 88
Author(s): Sandhya Tiwari, Edvin Fuglebakk, Siv Midtun Hollup, Lars Skjærven, Tristan Cragnolini, Svenn Helge Grindhaug, Kidane Tekle, Nathalie Reuter
Software Mentions: 1
Published: over 11 years ago

10.1186/1471-2105-10-29

Using least median of squares for structural superposition of flexible proteins
Cited by: 15
Author(s): Yu Shen Liu, Yi Fang, Karthik Ramani
Software Mentions: 1
Published: over 17 years ago

10.1186/1471-2105-13-S4-I1

Bioinformatics in Italy: BITS2011, the Eighth Annual Meeting of the Italian Society of Bioinformatics
Cited by: 2
Author(s): Paolo Romano, Manuela Helmer-Citterich
Software Mentions: 1
Published: over 14 years ago

10.1186/1471-2105-10-351

A structure filter for the Eukaryotic Linear Motif Resource
Cited by: 41
Author(s): Allegra Via, Cathryn M. Gould, Christine Gemünd, Toby J. Gibson, Manuela Helmer-Citterich
Software Mentions: 1
Published: almost 17 years ago

10.1186/1471-2105-11-S7-S16

Identification of a better Homo sapiens Class II HDAC inhibitor through binding energy calculations and descriptor analysis
Cited by: 20
Author(s): Usman Sumo Friend Tambunan, Evi Kristin Wulandari
Software Mentions: 1
Published: almost 16 years ago

10.1186/1471-2105-12-160

FunFOLD: an improved automated method for the prediction of ligand binding residues using 3D models of proteins
Cited by: 63
Author(s): Daniel B. Roche, Stuart J. Tetchner, Liam J. McGuffin
Software Mentions: 1
Published: about 15 years ago

10.1186/1471-2105-15-95

A local average distance descriptor for flexible protein structure comparison
Cited by: 7
Author(s): Hsin-Wei Wang, Chia-Han Chu, Wen-Ching Wang, Tun‐Wen Pai
Software Mentions: 1
Published: over 12 years ago

10.1186/1471-2105-15-S8-S2

Computational prediction of hinge axes in proteins
Cited by: 3
Author(s): Rittika Shamsuddin, Milka Doktorova, Sheila S. Jaswal, Audrey Lee-St. John, Kathryn A. McMenimen
Software Mentions: 1
Published: about 12 years ago

10.1186/1471-2105-12-S1-S31

Changed epitopes drive the antigenic drift for influenza A (H3N2) viruses
Cited by: 32
Author(s): Jhang Wei Huang, Jinn-Moon Yang
Software Mentions: 1
Published: over 15 years ago

10.1186/s12859-018-2346-4

An integrated strategy for identifying new targets and inferring the mechanism of action: taking rhein as an example
Cited by: 9
Author(s): Hao Sun, Yiting Shen, Guangwen Luo, Yuepiao Cai, Zheng Xiang
Software Mentions: 1
Published: almost 8 years ago

10.1186/1471-2105-15-112

Structural genomics analysis of uncharacterized protein families overrepresented in human gut bacteria identifies a novel glycoside hydrolase
Cited by: 12
Author(s): Anna Sheydina, Ruth Y Eberhardt, Daniel J. Rigden, Yuanyuan Chang, Zhanwen Li, Christian C Zmasek, Herbert L. Axelrod, Adam Godzik
Software Mentions: 1
Published: over 12 years ago

10.1186/1471-2105-11-426

TOPSAN: a collaborative annotation environment for structural genomics
Cited by: 13
Author(s): Dana Weekes, S. Sri Krishna, Constantina Bakolitsa, Ian A. Wilson, Adam Godzik, John Wooley
Software Mentions: 1
Published: almost 16 years ago

10.1186/s12859-015-0545-9

CHEXVIS: a tool for molecular channel extraction and visualization
Cited by: 67
Author(s): Talha Bin Masood, Sankaran Sandhya, Nagasuma Chandra, Vijay Natarajan
Software Mentions: 1
Published: over 11 years ago

10.1186/1471-2105-14-265

Two Pfam protein families characterized by a crystal structure of protein lpg2210 from Legionella pneumophila
Cited by: 3
Author(s): Penelope Coggill, Ruth Y Eberhardt, Alex Bateman, Yuanyuan Chang, Lukasz Jaroszewski, Adam Godzik, Debanu Das, Qingping Xu, Herbert L. Axelrod, L. Aravind, Alexey G. Murzin, Alex Bateman
Software Mentions: 1
Published: almost 13 years ago

10.1186/1471-2105-11-424

Computing H/D-Exchange rates of single residues from data of proteolytic fragments
Cited by: 43
Author(s): Ernst Althaus, Stefan Canzar, Carsten Ehrler, Mark R. Emmett, Andreas Karrenbauer, Alan G. Marshall, Anke Meyer-Bäse, Jeremiah D. Tipton, Hui Min Zhang
Software Mentions: 1
Published: about 16 years ago

10.1186/1471-2105-16-S1-S7

On the packing density of the unbound protein-protein interaction interface and its implications in dynamics
Cited by: 2
Author(s): Jau-Ji Lin, Zih Shin Lin, Jiann Yang Hwang, Tsun-Tsao Huang
Software Mentions: 1
Published: over 11 years ago

10.1186/1471-2105-12-S13-S22

Non-nucleosidic inhibition of Herpes simplex virus DNA polymerase: mechanistic insights into the anti-herpetic mode of action of herbal drug withaferin A
Cited by: 45
Author(s): Abhinav Grover, Vibhuti Agrawal, Ashutosh Shandilya, Virendra S. Bisaria, Durai Sundar
Software Mentions: 1
Published: over 14 years ago

10.1186/1471-2105-10-S1-S41

Co-evolution positions and rules for antigenic variants of human influenza A/H3N2 viruses
Cited by: 40
Author(s): Jhang Wei Huang, Chwan-Chuen King, Jinn-Moon Yang
Software Mentions: 1
Published: over 17 years ago

10.1186/1471-2105-10-32

VASCo: computation and visualization of annotated protein surface contacts
Cited by: 70
Author(s): Georg Steinkellner, Robert Rader, Gerhard G. Thallinger, Christoph Kratky, Karl Gruber
Software Mentions: 1
Published: over 17 years ago

10.1186/s12859-018-2317-9

RNAfitme: a webserver for modeling nucleobase and nucleoside residue conformation in fixed-backbone RNA structures
Cited by: 11
Author(s): Maciej Antczak, Tomasz Żok, Maciej Osowiecki, Mariusz Popenda, Ryszard W. Adamiak, Marta Szachniuk
Software Mentions: 1
Published: almost 8 years ago

10.1186/1471-2105-12-S13-S23

In silico modification of suberoylanilide hydroxamic acid (SAHA) as potential inhibitor for class II histone deacetylase (HDAC)
Cited by: 26
Author(s): Usman Sumo Friend Tambunan, N. Bramantya, Arli Aditya Parikesit
Software Mentions: 1
Published: over 14 years ago

10.1186/1471-2105-11-306

Beyond rotamers: a generative, probabilistic model of side chains in proteins
Cited by: 45
Author(s): Tim Harder, Wouter Boomsma, Martin Paluszewski, Jes Frellsen, Kristoffer E. Johansson, Thomas Hamelryck
Software Mentions: 1
Published: about 16 years ago

10.1186/s12859-016-1371-4

SCMBYK: prediction and characterization of bacterial tyrosine-kinases based on propensity scores of dipeptides
Cited by: 11
Author(s): Tamara Vasylenko, Yi Fan Liou, Po Chin Chiou, Hsiao Wei Chu, Yung Sung Lai, Yu Ling Chou, Hui Ling Huang, Shinn-Ying Ho
Software Mentions: 1
Published: over 9 years ago

10.1186/s12859-014-0370-6

PyTMs: a useful PyMOL plugin for modeling common post-translational modifications
Cited by: 77
Author(s): Andreas Warnecke, Tatyana Sandalova, Adnane Achour, Robert A. Harris
Software Mentions: 1
Published: over 11 years ago

10.1186/s12859-016-1033-6

Evolutionary relationships between heme-binding ferredoxin α + β barrels
Cited by: 8
Author(s): Giriraj Acharya, Gurmeet Kaur, S. Subramanian
Software Mentions: 1
Published: over 10 years ago

10.1186/s12859-016-1124-4

Detection and sequence/structure mapping of biophysical constraints to protein variation in saturated mutational libraries and protein sequence alignments with a dedicated server
Cited by: 18
Author(s): Luciano A. Abriata, Christophe Bovigny, Matteo Dal Peraro
Software Mentions: 1
Published: about 10 years ago

10.1186/s12859-015-0724-8

Development and validation of an epitope prediction tool for swine (PigMatrix) based on the pocket profile method
Cited by: 16
Author(s): Andrés H. Gutiérrez, William Martin, Chris Bailey‐Kellogg, Frances Terry, Leonard Moise, Anne S. De Groot
Software Mentions: 1
Published: almost 11 years ago

10.1186/1471-2105-6-202

PALSSE: A program to delineate linear secondary structural elements from protein structures
Cited by: 59
Author(s): Indraneel Majumdar, S. Sri Krishna, Nick V. Grishin
Software Mentions: 1
Published: about 21 years ago

10.1186/1741-7007-10-62

Crystal structure of the conserved domain of the DC lysosomal associated membrane protein: implications for the lysosomal glycocalyx
Cited by: 80
Author(s): Sonja Wilke, J. Krausze, Konrad Büssow
Software Mentions: 1
Published: about 14 years ago

10.1186/s12915-020-00885-2

Modified base-binding EVE and DCD domains: striking diversity of genomic contexts in prokaryotes and predicted involvement in a variety of cellular processes
Cited by: 4
Author(s): Ryan T. Bell, Yuri I. Wolf, Eugene V. Koonin
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12915-020-00936-8

Native-like membrane models of E. coli polar lipid extract shed light on the importance of lipid composition complexity
Cited by: 28
Author(s): Kristýna Pluháčková, Andreas Hörner
Software Mentions: 1
Published: over 5 years ago

10.1186/s12915-016-0313-y

Oligomeric interface modulation causes misregulation of purine 5´-nucleotidase in relapsed leukemia
Cited by: 9
Author(s): Aleš Hnı́zda, Jana Škerlová, Milan Fábry, Petr Pachl, Martina Šinalová, Lukáš Vrzal, Petr Man, Petr Novák, P. Řezáčová, Václav Veverka
Software Mentions: 1
Published: almost 10 years ago

10.1186/s12915-017-0464-5

Outer membrane protein folding from an energy landscape perspective
Cited by: 55
Author(s): Bob Schiffrin, David J. Brockwell, Sheena E. Radford
Software Mentions: 1
Published: over 8 years ago

10.1186/s12915-020-00920-2

Crystal structure of the yeast heterodimeric ADAT2/3 deaminase
Cited by: 15
Author(s): Xiwen Liu, Ruoyu Chen, Yujie Sun, Ran Chen, Jie Zhou, Qingnan Tian, Xiaoma Tao, Zhang Zhang, Guan‐Zheng Luo, Wei Xie
Software Mentions: 1
Published: over 5 years ago

10.1186/s12915-020-00896-z

Speciation and adaptive evolution reshape antioxidant enzymatic system diversity across the phylum Nematoda
Cited by: 10
Author(s): Liang Xu, Jian Yang, Meng Xu, Dai Shan, Zhongdao Wu, Dongjuan Yuan
Software Mentions: 1
Published: over 5 years ago

10.1186/1741-7007-8-134

The nucleotide addition cycle of RNA polymerase is controlled by two molecular hinges in the Bridge Helix domain
Cited by: 48
Author(s): Robert O. J. Weinzierl
Software Mentions: 1
Published: almost 16 years ago

10.1186/1741-7007-8-70

Expansion of ribosomally produced natural products: a nitrile hydratase- and Nif11-related precursor family
Cited by: 124
Author(s): Daniel H. Haft, Malay Kumar Basu, Douglas A. Mitchell
Software Mentions: 1
Published: about 16 years ago

10.1186/s12915-017-0446-7

A yeast two-hybrid system for the screening and characterization of small-molecule inhibitors of protein–protein interactions identifies a novel putative Mdm2-binding site in p53
Cited by: 28
Author(s): Jin Huei Wong, Mohammad Alfatah, Mei Fang Sin, Hong May Sim, Chandra Verma, David P. Lane, Prakash Arumugam
Software Mentions: 1
Published: almost 9 years ago

10.1186/1741-7007-9-7

The activation mechanism of Irga6, an interferon-inducible GTPase contributing to mouse resistance against Toxoplasma gondii
Cited by: 28
Author(s): Nikolaus Pawlowski, Aliaksandr Khaminets, Julia P. Hunn, Natasa Papic, Andreas Schmidt, Revathy C. Uthaiah, Rita Lange, Gabriela Vopper, Sascha Martens, Eva Wolf, Jonathan C. Howard
Software Mentions: 1
Published: over 15 years ago

10.1186/2046-1682-5-13

A minimal ligand binding pocket within a network of correlated mutations identified by multiple sequence and structural analysis of G protein coupled receptors
Cited by: 7
Author(s): Subhodeep Moitra, Kalyan Tirupula, Judith Klein‐Seetharaman, Christopher J. Langmead
Software Mentions: 1
Published: about 14 years ago

10.1186/2046-1682-5-2

Protein dynamics at Eph receptor-ligand interfaces as revealed by crystallography, NMR and MD simulations
Cited by: 23
Author(s): Haina Qin, Liangzhong Lim, Jianxing Song
Software Mentions: 1
Published: over 14 years ago

10.1186/1472-6750-13-71

Systematic screening of glycosylation- and trafficking-associated gene knockouts in Saccharomyces cerevisiaeidentifies mutants with improved heterologous exocellulase activity and host secretion
Cited by: 31
Author(s): Tzi‐Yuan Wang, Chih-Jen Huang, Hsin‐Liang Chen, Po-Chun Ho, Huei-Mien Ke, Hsing-Yi Cho, Sz-Kai Ruan, Kuo-Yen Hung, I-Li Wang, Ya-Wun Cai, Huang‐Mo Sung, Wen-Hsiung Li, Ming-Che Shih
Software Mentions: 1
Published: almost 13 years ago

10.1186/s12896-015-0217-x

Defining the complementarities between antibodies and haptens to refine our understanding and aid the prediction of a successful binding interaction
Cited by: 13
Author(s): Mohammed M. Al Qaraghuli, Soumya Palliyil, Gillian Broadbent, David C. Cullen, Keith A. Charlton, A.J. Porter
Software Mentions: 1
Published: almost 11 years ago

10.1186/s12896-018-0420-7

Effects of substrate binding site residue substitutions of xynA from Bacillus amyloliquefaciens on substrate specificity
Cited by: 10
Author(s): Anil S. Prajapati, V A Pawar, Ketankumar Panchal, Ankit P. Sudhir, Bhaumik R. Dave, Darshan H. Patel, R. B. Subramanian
Software Mentions: 1
Published: over 8 years ago

10.1186/s12896-019-0520-z

Surface patches on recombinant erythropoietin predict protein solubility: engineering proteins to minimise aggregation
Cited by: 7
Author(s): Manuel Alejandro Carballo-Amador, Edward A. McKenzie, Alan J. Dickson, Jim Warwicker
Software Mentions: 1
Published: over 7 years ago

10.1186/s12896-015-0214-0

A novel eurythermic and thermostale lipase LipM from Pseudomonas moraviensis M9 and its application in the partial hydrolysis of algal oil
Cited by: 22
Author(s): Wuyi Yang, Cao Hai, Li Xu, Houjin Zhang, Yunjun Yan
Software Mentions: 1
Published: almost 11 years ago

10.1186/s12896-017-0389-7

Conversion of an inactive xylose isomerase into a functional enzyme by co-expression of GroEL-GroES chaperonins in Saccharomyces cerevisiae
Cited by: 22
Author(s): Beatriz Temer, Leandro Vieira dos Santos, Victor Augusti Negri, Juliana Pimentel Galhardo, Pedro Henrique Mello Magalhães, Juliana José, Cidnei Marschalk, Thamy Lívia Ribeiro Corrêa, Marcelo Falsarella Carazzolle, Gonçalo Amarante Guimarães Pereira
Software Mentions: 1
Published: almost 9 years ago

10.1186/s12896-019-0542-6

Improved the expression level of active transglutaminase by directional increasing copy of mtg gene in Pichia pastoris
Cited by: 6
Author(s): Xiaoping Song, Changsheng Shao, Yugang Guo, Yajie Wang, Jingjing Cai
Software Mentions: 1
Published: about 7 years ago

10.1186/s12896-021-00701-x

Optimization of expression, purification and secretion of functional recombinant human growth hormone in Escherichia coli using modified staphylococcal protein a signal peptide
Cited by: 7
Author(s): Garshasb Rigi, Amin Rostami, Habib Ghomi, Gholamreza Ahmadian, V.S. Mirbagheri, Meisam Jeiranikhameneh, Majid Vahed, Sahel Rahimi
Software Mentions: 1
Published: almost 5 years ago

10.1186/s12896-016-0310-9

Improvement of alkalophilicity of an alkaline xylanase Xyn11A-LC from Bacillus sp. SN5 by random mutation and Glu135 saturation mutagenesis
Cited by: 19
Author(s): Wenqin Bai, Yufan Cao, Jun Liu, Qinhong Wang, Zhenhu Jia
Software Mentions: 1
Published: almost 10 years ago

10.1186/s12896-019-0553-3

Structure-based engineering of heparinase I with improved specific activity for degrading heparin
Cited by: 5
Author(s): Chuan Zhang, Baocheng Yang, Wenting Liu, Zhongyuan Li, Yajian Song, Tongcun Zhang, Xue‐Gang Luo
Software Mentions: 1
Published: about 7 years ago

10.1186/s12896-017-0396-8

Production and purification of chimeric HBc virus-like particles carrying influenza virus LAH domain as vaccine candidates
Cited by: 22
Author(s): Andris Kazāks, I-Na Lu, Sophie Farinelle, Alex Ramirez, Vincenzo Crescente, Benjamin A. F. Bláha, Olotu W. Ogonah, Tarit Mukhopadhyay, Mapi Perez de Obanos, Alejandro Krimer, Ināra Akopjana, Jānis Bogans, Velta Ose, Anna Kirsteina, Tatjana Kazaka, Nicola J. Stonehouse, David J. Rowlands, Claude P. Muller, Kaspars Tārs, William Rosenberg
Software Mentions: 1
Published: almost 9 years ago

10.1186/s12885-016-2108-5

Aberrant KDM5B expression promotes aggressive breast cancer through MALAT1 overexpression and downregulation of hsa-miR-448
Cited by: 100
Author(s): Oluwaseun Adebayo Bamodu, Wen Chien Huang, Wei Hwa Lee, Alexander T.H. Wu, Liang Shun Wang, Michael Hsiao, Chi‐Tai Yeh, Tsu Yi Chao
Software Mentions: 1
Published: over 10 years ago

10.1186/s12885-019-6013-6

Parkin gene mutations are not common, but its epigenetic inactivation is a frequent event and predicts poor survival in advanced breast cancer patients
Cited by: 13
Author(s): Khushnuma Wahabi, Ahmad Perwez, Shabeena Kamarudheen, Zafar Iqbal Bhat, Anurag Mehta, M. Moshahid Alam Rizvi
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12885-019-6477-4

Bag-1 stimulates Bad phosphorylation through activation of Akt and Raf kinases to mediate cell survival in breast cancer
Cited by: 18
Author(s): Tugba Kizilboga, Emine Arzu Baskale, Jale Yıldız, İzzet Mehmet Akçay, Ebru Zemheri, Nisan Denizce Can, C. Ozden, Salih Demir, Fikret Ezbercı, Gizem Dinler Doğanay
Software Mentions: 1
Published: over 6 years ago

10.1186/s12885-018-5142-7

KRas4B-PDE6δ complex stabilization by small molecules obtained by virtual screening affects Ras signaling in pancreatic cancer
Cited by: 18
Author(s): Diana Casique‐Aguirre, Paola Briseño-Díaz, Ponciano García-Gutiérrez, Claudia H. González-De la Rosa, Reyna Sara Quintero-Barceinas, Arturo Rojo-Domı́nguez, Irene Vergara, L. Medina, José Correa‐Basurto, Martiniano Bello, Rosaura Hernández‐Rivas, María del RocioThompson-Bonilla, Miguel Vargas
Software Mentions: 1
Published: over 7 years ago

10.1186/s12885-019-5532-5

Protein interaction disruption in cancer
Cited by: 8
Author(s): Matthew Ruffalo, Ziv Bar‐Joseph
Software Mentions: 1
Published: over 7 years ago

10.1186/s12885-021-08174-z

Robust expression of LINE-1 retrotransposon encoded proteins in oral squamous cell carcinoma
Cited by: 2
Author(s): Koel Mukherjee, Debpali Sur, Abhijeet Singh, Suresh Rai, Neeladrisingha Das, Rakshanya Sekar, Srinu Narindi, Vandana Dhingra, Bhanwar Lal Jat, K V Vinu Balraam, Saurabh Agarwal, Prabhat Kumar Mandal
Software Mentions: 1
Published: about 5 years ago

10.1186/s12885-018-4704-z

Natural product derivative Gossypolone inhibits Musashi family of RNA-binding proteins
Cited by: 35
Author(s): Lan Lan, Hao Líu, Amber Rae Smith, Carl Appelman, Yu Jiao, Sarah Line Larsen, Rebecca T. Marquez, Xiaoqing Wu, Frank Y. Liu, Philip Gao, Ragul Gowthaman, John Karanicolas, Roberto N. De Guzman, Steven A. Rogers, Jeffrey Aubé, Kristi L. Neufeld, Liang Xu
Software Mentions: 1
Published: about 8 years ago

10.1186/s12885-019-6056-8

Generation of dual specific bivalent BiTEs (dbBIspecific T-cell engaging antibodies) for cellular immunotherapy
Cited by: 7
Author(s): Maciej Kujawski, Lin Li, Supriyo Bhattacharya, Patty Wong, Wen‐Hwa Lee, Lindsay Williams, Harry Li, Junie Chea, Kofi Poku, Nicole Bowles, Nagarajan Vaidehi, Paul J. Yazaki, John E. Shively
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12885-019-5845-4

A germline mutation in Rab43 gene identified from a cancer family predisposes to a hereditary liver-colon cancer syndrome
Cited by: 4
Author(s): Yanting Jiang, Yue Sun, Jianbo Hu, Nan Yu, Hui Liu, Jiankun Fan, Xuelian Ning, Yilan Li, Baogang Liu, Yihua Sun, Jinwei Zhang, Xiaohong Qiu, Songbin Fu, Chunlan Zhou, Hui Xu
Software Mentions: 1
Published: about 7 years ago

10.1186/1471-2121-14-27

Arginine68 is an essential residue for the C-terminal cleavage of human Atg8 family proteins
Cited by: 16
Author(s): Chao Liu, Hongshen Ma, Jiaxue Wu, Qiang Huang, Jun O. Liu, Yu Liu
Software Mentions: 1
Published: about 13 years ago

10.1186/s13065-021-00758-x

Antibacterial and antioxidant activities of extracts and isolated compounds from the roots extract of Cucumis prophetarum and in silico study on DNA gyrase and human peroxiredoxin 5
Cited by: 8
Author(s): Wario Galma, Milkyas Endale, Emebet Getaneh, Rajalakshmanan Eswaramoorthy, Temesgen Assefa, Yadessa Melaku
Software Mentions: 1
Published: over 5 years ago

10.1186/s13065-021-00766-x

Molecular docking, chemo-informatic properties, alpha-amylase, and lipase inhibition studies of benzodioxol derivatives
Cited by: 12
Author(s): Mohammed Hawash, Nidal Jaradat, Suhaib Shekfeh, Murad Abualhasan, Ahmad Eid, Linda Issa
Software Mentions: 1
Published: about 5 years ago

10.1186/s13065-019-0582-y

Molecular docking and simulation of Zika virus NS3 helicase
Cited by: 15
Author(s): Syed Lal Badshah, Nasir Ahmad, Ashfaq Ur Rehman, Khalid Khan, Asad Ullah, Abdulrhman Alsayari, Abdullatif Bin Muhsinah, Yahia N. Mabkhot
Software Mentions: 1
Published: about 7 years ago

10.1186/s13065-019-0532-8

Design, synthesis and evaluation of novel 3,5-disubstituted benzamide derivatives as allosteric glucokinase activators
Cited by: 14
Author(s): Ajmer Singh Grewal, Rajeev Kharb, Devendra Prasad, Jagdeep Singh Dua, Viney Lather
Software Mentions: 1
Published: over 7 years ago

10.1186/s12906-018-2312-8

Efficacy of Andrographis paniculata against extended spectrum β-lactamase (ESBL) producing E. coli
Cited by: 28
Author(s): Ubaid Rasool, Shivam Priya, Afsana Parveen, Saroj Kumar Sah, S. Hemalatha
Software Mentions: 1
Published: almost 8 years ago

10.1186/1472-6882-14-89

Role of berberine in anti-bacterial as a high-affinity LPS antagonist binding to TLR4/MD-2 receptor
Cited by: 67
Author(s): Ming Chu, Ran Ding, Zhi‐gang Chu, Mingbo Zhang, Xiaoyan Liu, Shao-Hua Xie, Yuanzheng Zhai, Yuedan Wang
Software Mentions: 1
Published: over 12 years ago

10.1186/1472-6823-14-16

A case of Aromatase deficiency due to a novel CYP19A1 mutation
Cited by: 35
Author(s): Lucia Gagliardi, Hamish S. Scott, Feng Jiang, David J. Torpy
Software Mentions: 1
Published: over 12 years ago

10.1186/s12862-019-1461-9

Insights into body size variation in cetaceans from the evolution of body-size-related genes
Cited by: 10
Author(s): Yingying Sun, Yanzhi Liu, Xiaohui Sun, Yurui Lin, Daiqing Yin, Shixia Xu, Guang Yang
Software Mentions: 1
Published: about 7 years ago

10.1186/1471-2148-10-365

Chlorophyll-binding proteins revisited - a multigenic family of light-harvesting and stress proteins from a brown algal perspective
Cited by: 91
Author(s): Simon M. Dittami, Gurvan Michel, Jonas Collén, Catherine Boyen, Thierry Tonon
Software Mentions: 1
Published: over 16 years ago

10.1186/s12862-015-0490-2

Divergence and adaptive evolution of the gibberellin oxidase genes in plants
Cited by: 41
Author(s): Yuan Huang, Xi Wang, Song Ge, Guang‐Yuan Rao
Software Mentions: 1
Published: almost 11 years ago

10.1186/1471-2148-12-4

Evolution, expansion and expression of the Kunitz/BPTI gene family associated with long-term blood feeding in Ixodes Scapularis
Cited by: 54
Author(s): Shao‐Xing Dai, Ai-Di Zhang, Jing‐Fei Huang
Software Mentions: 1
Published: over 14 years ago

10.1186/1471-2148-11-149

Molecular evolution of the vertebrate TLR1 gene family - a complex history of gene duplication, gene conversion, positive selection and co-evolution
Cited by: 62
Author(s): Yinhua Huang, Nicholas D. Temperley, Liming Ren, Jacqueline Smith, Ning Li, David W. Burt
Software Mentions: 1
Published: about 15 years ago

10.1186/s12862-015-0337-x

Phylogeny and evolution of plant macrophage migration inhibitory factor/D-dopachrome tautomerase-like proteins
Cited by: 30
Author(s): Ralph Panstruga, Kira Baumgarten, Jürgen Bernhagen
Software Mentions: 1
Published: over 11 years ago

10.1186/1471-2148-11-273

The UlaG protein family defines novel structural and functional motifs grafted on an ancient RNase fold
Cited by: 7
Author(s): Francisco Fernández, Fernando Garcés, Miguel López-Estepa, Juan Aguilar, Laura Baldomà, Miquel Coll, Josefa Badı́a, M. Cristina Vega
Software Mentions: 1
Published: over 15 years ago

10.1186/1471-2148-12-66

Molecular evolution of pentatricopeptide repeat genes reveals truncation in species lacking an editing target and structural domains under distinct selective pressures
Cited by: 30
Author(s): Michael L. Hayes, Karolyn Giang, R. Michael Mulligan
Software Mentions: 1
Published: about 14 years ago

10.1186/s12862-016-0823-9

Structural differences and differential expression among rhabdomeric opsins reveal functional change after gene duplication in the bay scallop, Argopecten irradians (Pectinidae)
Cited by: 8
Author(s): Anita J. Porath-Krause, Autum N. Pairett, Davide Faggionato, Bhagyashree S. Birla, Kalyanasundaram Sankar, Jeanne M. Serb
Software Mentions: 1
Published: over 9 years ago

10.1186/s13104-018-3513-4

Investigating the functionality of a ribosome-binding mutant of NAA15 using Saccharomyces cerevisiae
Cited by: 9
Author(s): Sylvia Varland, Thomas Arnesen
Software Mentions: 1
Published: about 8 years ago

10.1186/1756-0500-3-271

SECRET domain of variola virus CrmB protein can be a member of poxviral type II chemokine-binding proteins family
Cited by: 18
Author(s): Денис Антонец, T. S. Nepomnyashchikh, С. Н. Щелкунов
Software Mentions: 1
Published: almost 16 years ago

10.1186/1756-0500-2-251

Crystallographic structure of ubiquitin in complex with cadmium ions
Cited by: 6
Author(s): Insaf Ahmed Qureshi, François Ferrón, Cheah Chen Seh, Pierina Cheung, Julien Lescar
Software Mentions: 1
Published: over 17 years ago

10.1186/s13104-015-1483-3

PyMine: a PyMOL plugin to integrate and visualize data for drug discovery
Cited by: 31
Author(s): Rajan Chaudhari, Zhijun Li
Software Mentions: 1
Published: almost 11 years ago

10.1186/s13104-021-05461-7

A virtual alternative to molecular model sets: a beginners’ guide to constructing and visualizing molecules in open-source molecular graphics software
Cited by: 5
Author(s): Siripreeya Phankingthongkum, Taweetham Limpanuparb
Software Mentions: 1
Published: over 5 years ago

10.1186/s13104-016-2149-5

GP0.4 from bacteriophage T7: in silico characterisation of its structure and interaction with E. coli FtsZ
Cited by: 3
Author(s): Adam J Simpkin, Daniel J. Rigden
Software Mentions: 1
Published: about 10 years ago

10.1186/1756-0500-4-173

Severe forms of partial androgen insensitivity syndrome due to p.L830F novel mutation in androgen receptor gene in a Brazilian family
Cited by: 10
Author(s): Reginaldo José Petroli, Andréa T. Maciel‐Guerra, Fernanda Caroline Soardi, Flávia Leme de Calais, Gil Guerra, Maricilda Palandi de Mello
Software Mentions: 1
Published: about 15 years ago

10.1186/1472-6807-9-44

Amyloidogenic determinants are usually not buried
Cited by: 134
Author(s): Kimon Frousios, Vassiliki A. Iconomidou, Carolina-Maria Karletidi, Stavros J. Hamodrakas
Software Mentions: 1
Published: about 17 years ago

10.1186/1472-6807-13-S1-S2

Modeling protein conformational transitions by a combination of coarse-grained normal mode analysis and robotics-inspired methods
Cited by: 41
Author(s): Ibrahim Al-Bluwi, Marc Vaisset, Thierry Siméon, Juan Cortés
Software Mentions: 1
Published: almost 13 years ago

10.1186/1472-6807-12-6

Comparison of tertiary structures of proteins in protein-protein complexes with unbound forms suggests prevalence of allostery in signalling proteins
Cited by: 22
Author(s): Lakshmipuram S. Swapna, Swapnil Mahajan, Alexandre G. de Brevern, Narayanaswamy Srinivasan
Software Mentions: 1
Published: over 14 years ago